Starting phenix.real_space_refine on Sat Mar 7 08:40:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bst_30166/03_2026/7bst_30166.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bst_30166/03_2026/7bst_30166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bst_30166/03_2026/7bst_30166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bst_30166/03_2026/7bst_30166.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bst_30166/03_2026/7bst_30166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bst_30166/03_2026/7bst_30166.map" } resolution = 4.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15738 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 18012 2.51 5 N 4729 2.21 5 O 5461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28266 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 7906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7906 Classifications: {'peptide': 975} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 10, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 943} Chain breaks: 5 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "C" Number of atoms: 8042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 8042 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 13, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 956} Chain breaks: 4 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3732 Classifications: {'peptide': 472} Link IDs: {'CIS': 18, 'PTRANS': 13, 'TRANS': 440} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3735 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 18, 'PTRANS': 13, 'TRANS': 441} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 876 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "G" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 876 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "A" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3099 Classifications: {'peptide': 384} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 359} Time building chain proxies: 5.80, per 1000 atoms: 0.21 Number of scatterers: 28266 At special positions: 0 Unit cell: (129.6, 184.95, 162, 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 64 16.00 O 5461 8.00 N 4729 7.00 C 18012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.0 seconds 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6722 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 22 sheets defined 47.2% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'B' and resid 32 through 48 Processing helix chain 'B' and resid 56 through 73 removed outlier: 3.946A pdb=" N MET B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU B 61 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 89 Processing helix chain 'B' and resid 95 through 105 removed outlier: 3.590A pdb=" N ILE B 103 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.609A pdb=" N ASN B 132 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 222 through 226 removed outlier: 3.895A pdb=" N PHE B 225 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 248 removed outlier: 3.514A pdb=" N PHE B 248 " --> pdb=" O THR B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 260 removed outlier: 3.536A pdb=" N TYR B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 293 removed outlier: 3.698A pdb=" N GLU B 281 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 Processing helix chain 'B' and resid 315 through 326 removed outlier: 3.861A pdb=" N GLU B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 349 removed outlier: 3.529A pdb=" N GLU B 349 " --> pdb=" O GLN B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 373 removed outlier: 3.825A pdb=" N ASN B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.745A pdb=" N TYR B 399 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN B 400 " --> pdb=" O PRO B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.705A pdb=" N GLN B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYS B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 454 Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.978A pdb=" N ALA B 466 " --> pdb=" O VAL B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 491 Processing helix chain 'B' and resid 495 through 500 removed outlier: 3.823A pdb=" N SER B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 removed outlier: 3.506A pdb=" N GLU B 515 " --> pdb=" O MET B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 564 removed outlier: 3.852A pdb=" N THR B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 620 Processing helix chain 'B' and resid 632 through 647 Processing helix chain 'B' and resid 678 through 687 Processing helix chain 'B' and resid 708 through 718 Processing helix chain 'B' and resid 723 through 728 removed outlier: 4.050A pdb=" N VAL B 728 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 removed outlier: 3.717A pdb=" N MET B 737 " --> pdb=" O TYR B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 763 removed outlier: 3.771A pdb=" N VAL B 755 " --> pdb=" O GLY B 751 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 769 Processing helix chain 'B' and resid 771 through 793 removed outlier: 3.595A pdb=" N PHE B 778 " --> pdb=" O GLU B 774 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU B 784 " --> pdb=" O LYS B 780 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE B 791 " --> pdb=" O ARG B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 805 removed outlier: 3.994A pdb=" N ALA B 799 " --> pdb=" O TYR B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 820 removed outlier: 4.499A pdb=" N PHE B 818 " --> pdb=" O ALA B 814 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B 820 " --> pdb=" O GLU B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 835 removed outlier: 3.778A pdb=" N GLN B 833 " --> pdb=" O PHE B 829 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 835 " --> pdb=" O GLU B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 858 removed outlier: 3.568A pdb=" N ARG B 847 " --> pdb=" O ILE B 843 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE B 853 " --> pdb=" O ALA B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 900 removed outlier: 3.557A pdb=" N PHE B 898 " --> pdb=" O LEU B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 919 removed outlier: 3.742A pdb=" N ARG B 919 " --> pdb=" O LYS B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 926 No H-bonds generated for 'chain 'B' and resid 924 through 926' Processing helix chain 'B' and resid 927 through 938 removed outlier: 3.810A pdb=" N VAL B 932 " --> pdb=" O GLU B 928 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 971 removed outlier: 3.514A pdb=" N ILE B 949 " --> pdb=" O ASP B 945 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 966 " --> pdb=" O GLN B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 990 removed outlier: 3.645A pdb=" N ARG B 984 " --> pdb=" O LYS B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1031 Processing helix chain 'C' and resid 32 through 48 removed outlier: 3.556A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 72 Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 172 through 178 removed outlier: 3.892A pdb=" N ASN C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.740A pdb=" N LYS C 196 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR C 197 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 198 " --> pdb=" O PHE C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 193 through 198' Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.590A pdb=" N SER C 222 " --> pdb=" O ASP C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 247 Processing helix chain 'C' and resid 249 through 260 Processing helix chain 'C' and resid 273 through 294 Processing helix chain 'C' and resid 298 through 302 Processing helix chain 'C' and resid 313 through 326 removed outlier: 3.530A pdb=" N SER C 317 " --> pdb=" O LYS C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 350 removed outlier: 3.525A pdb=" N GLN C 345 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 396 through 401 removed outlier: 3.535A pdb=" N TYR C 399 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN C 400 " --> pdb=" O PRO C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 414 removed outlier: 4.489A pdb=" N GLN C 414 " --> pdb=" O HIS C 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 411 through 414' Processing helix chain 'C' and resid 415 through 425 removed outlier: 3.696A pdb=" N GLN C 419 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 454 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 486 through 491 Processing helix chain 'C' and resid 494 through 501 Processing helix chain 'C' and resid 509 through 528 removed outlier: 3.551A pdb=" N TYR C 519 " --> pdb=" O GLU C 515 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ARG C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLN C 526 " --> pdb=" O ASN C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 569 removed outlier: 3.691A pdb=" N ALA C 552 " --> pdb=" O ASP C 548 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER C 568 " --> pdb=" O ALA C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 623 Processing helix chain 'C' and resid 630 through 647 Processing helix chain 'C' and resid 680 through 687 Processing helix chain 'C' and resid 708 through 720 Processing helix chain 'C' and resid 723 through 728 Processing helix chain 'C' and resid 733 through 738 Processing helix chain 'C' and resid 752 through 763 removed outlier: 3.547A pdb=" N ARG C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 793 removed outlier: 4.176A pdb=" N GLU C 784 " --> pdb=" O LYS C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 804 Processing helix chain 'C' and resid 805 through 807 No H-bonds generated for 'chain 'C' and resid 805 through 807' Processing helix chain 'C' and resid 811 through 821 Processing helix chain 'C' and resid 825 through 835 removed outlier: 3.509A pdb=" N ILE C 835 " --> pdb=" O GLU C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 857 Processing helix chain 'C' and resid 890 through 898 Processing helix chain 'C' and resid 913 through 921 removed outlier: 3.927A pdb=" N LEU C 917 " --> pdb=" O GLU C 913 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG C 919 " --> pdb=" O LYS C 915 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 921 " --> pdb=" O LEU C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 938 removed outlier: 3.659A pdb=" N VAL C 931 " --> pdb=" O LYS C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 943 Processing helix chain 'C' and resid 945 through 971 removed outlier: 4.018A pdb=" N ILE C 949 " --> pdb=" O ASP C 945 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE C 950 " --> pdb=" O LYS C 946 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP C 951 " --> pdb=" O ALA C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 989 Processing helix chain 'C' and resid 1016 through 1031 Processing helix chain 'D' and resid 12 through 23 removed outlier: 3.994A pdb=" N ILE D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 53 removed outlier: 3.847A pdb=" N PHE D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN D 34 " --> pdb=" O TRP D 30 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR D 35 " --> pdb=" O ASP D 31 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 146 through 163 Processing helix chain 'D' and resid 178 through 185 Processing helix chain 'D' and resid 185 through 190 removed outlier: 4.422A pdb=" N ALA D 189 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 Processing helix chain 'D' and resid 256 through 267 removed outlier: 3.690A pdb=" N LEU D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET D 267 " --> pdb=" O ALA D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 271 removed outlier: 3.994A pdb=" N ASN D 271 " --> pdb=" O PHE D 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 268 through 271' Processing helix chain 'D' and resid 320 through 324 removed outlier: 3.654A pdb=" N ALA D 324 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 removed outlier: 3.847A pdb=" N VAL D 340 " --> pdb=" O ASP D 336 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 344 " --> pdb=" O VAL D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 378 removed outlier: 3.706A pdb=" N GLU D 368 " --> pdb=" O ARG D 364 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN D 378 " --> pdb=" O TYR D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 444 removed outlier: 3.965A pdb=" N ILE D 439 " --> pdb=" O HIS D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 508 removed outlier: 4.063A pdb=" N LEU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN D 489 " --> pdb=" O ILE D 485 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE D 499 " --> pdb=" O THR D 495 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP D 507 " --> pdb=" O ARG D 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 22 removed outlier: 3.570A pdb=" N ILE E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 54 removed outlier: 4.322A pdb=" N PHE E 32 " --> pdb=" O ASP E 28 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN E 34 " --> pdb=" O TRP E 30 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR E 35 " --> pdb=" O ASP E 31 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER E 50 " --> pdb=" O SER E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 115 through 121 Processing helix chain 'E' and resid 146 through 163 removed outlier: 3.792A pdb=" N LYS E 150 " --> pdb=" O THR E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 177 removed outlier: 3.584A pdb=" N PHE E 177 " --> pdb=" O ILE E 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 174 through 177' Processing helix chain 'E' and resid 178 through 186 removed outlier: 3.876A pdb=" N PHE E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 214 Processing helix chain 'E' and resid 231 through 239 removed outlier: 3.832A pdb=" N GLN E 236 " --> pdb=" O SER E 232 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA E 237 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 270 removed outlier: 3.816A pdb=" N MET E 267 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE E 268 " --> pdb=" O ARG E 264 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS E 270 " --> pdb=" O ASN E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 320 removed outlier: 4.148A pdb=" N ILE E 318 " --> pdb=" O PRO E 315 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP E 320 " --> pdb=" O LEU E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 344 removed outlier: 4.123A pdb=" N PHE E 339 " --> pdb=" O ALA E 335 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL E 340 " --> pdb=" O ASP E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 376 removed outlier: 4.208A pdb=" N LYS E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE E 371 " --> pdb=" O ALA E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 445 removed outlier: 3.881A pdb=" N ILE E 439 " --> pdb=" O HIS E 435 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER E 445 " --> pdb=" O GLN E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 507 removed outlier: 3.677A pdb=" N LEU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN E 489 " --> pdb=" O ILE E 485 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA E 490 " --> pdb=" O ALA E 486 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 499 " --> pdb=" O THR E 495 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 24 removed outlier: 3.682A pdb=" N VAL F 10 " --> pdb=" O THR F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 48 through 58 removed outlier: 3.811A pdb=" N VAL F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 71 Processing helix chain 'F' and resid 76 through 105 removed outlier: 4.569A pdb=" N ASN F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.682A pdb=" N VAL G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 41 Processing helix chain 'G' and resid 48 through 58 removed outlier: 3.811A pdb=" N VAL G 55 " --> pdb=" O ASP G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 Processing helix chain 'G' and resid 76 through 105 removed outlier: 4.569A pdb=" N ASN G 102 " --> pdb=" O GLU G 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 removed outlier: 3.803A pdb=" N ASN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 4.407A pdb=" N PHE A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 126' Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 157 through 190 removed outlier: 4.316A pdb=" N ILE A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.886A pdb=" N VAL A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 318 removed outlier: 3.629A pdb=" N ILE A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.537A pdb=" N LEU A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 369 removed outlier: 3.836A pdb=" N GLN A 355 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 394 removed outlier: 4.026A pdb=" N LEU A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.600A pdb=" N GLU B 50 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B 152 " --> pdb=" O GLN B 163 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLN B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE B 154 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 9.868A pdb=" N LEU B 200 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU B 161 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL B 202 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN B 163 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N SER B 204 " --> pdb=" O GLN B 163 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU B 165 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AA3, first strand: chain 'B' and resid 229 through 230 removed outlier: 4.234A pdb=" N TRP B 229 " --> pdb=" O ILE B 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 261 through 263 Processing sheet with id=AA5, first strand: chain 'B' and resid 378 through 381 removed outlier: 4.253A pdb=" N ASP B 408 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 378 through 381 removed outlier: 4.253A pdb=" N ASP B 408 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N PHE B 434 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N PHE B 407 " --> pdb=" O PHE B 434 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR B 304 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS B 459 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 474 through 477 removed outlier: 6.929A pdb=" N LYS B 474 " --> pdb=" O GLY B 700 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE B 702 " --> pdb=" O LYS B 474 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS B 476 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR B 704 " --> pdb=" O LYS B 476 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN B 669 " --> pdb=" O PHE B 699 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN B 539 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR B 670 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET B 541 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 672 " --> pdb=" O MET B 541 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 576 through 578 removed outlier: 3.507A pdb=" N ILE B 654 " --> pdb=" O ALA B 577 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 112 Processing sheet with id=AB1, first strand: chain 'C' and resid 134 through 138 removed outlier: 3.686A pdb=" N VAL C 162 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 156 " --> pdb=" O PRO C 160 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 204 " --> pdb=" O GLU C 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 261 through 264 removed outlier: 3.524A pdb=" N THR C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 381 through 382 removed outlier: 3.624A pdb=" N THR C 381 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL C 403 " --> pdb=" O TYR C 430 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N PHE C 432 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N PHE C 405 " --> pdb=" O PHE C 432 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE C 434 " --> pdb=" O PHE C 405 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE C 407 " --> pdb=" O PHE C 434 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N TYR C 304 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N SER C 460 " --> pdb=" O TYR C 304 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP C 306 " --> pdb=" O SER C 460 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 477 through 479 removed outlier: 6.770A pdb=" N ASN C 669 " --> pdb=" O ASN C 701 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL C 703 " --> pdb=" O ASN C 669 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU C 671 " --> pdb=" O VAL C 703 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN C 539 " --> pdb=" O LEU C 668 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR C 670 " --> pdb=" O ASN C 539 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET C 541 " --> pdb=" O THR C 670 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C 672 " --> pdb=" O MET C 541 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA C 540 " --> pdb=" O LEU C 653 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL C 655 " --> pdb=" O ALA C 540 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU C 542 " --> pdb=" O VAL C 655 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA C 577 " --> pdb=" O ILE C 654 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 224 through 226 removed outlier: 6.850A pdb=" N GLY D 252 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 298 through 300 removed outlier: 3.566A pdb=" N ILE D 299 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA D 354 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER D 405 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL D 381 " --> pdb=" O SER D 405 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 251 through 254 Processing sheet with id=AB8, first strand: chain 'E' and resid 355 through 357 Processing sheet with id=AB9, first strand: chain 'A' and resid 17 through 20 Processing sheet with id=AC1, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.850A pdb=" N LYS A 99 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 202 through 205 removed outlier: 3.998A pdb=" N GLU A 202 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 249 through 251 removed outlier: 4.477A pdb=" N ASP A 249 " --> pdb=" O TRP A 233 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 284 through 287 removed outlier: 3.942A pdb=" N ALA A 285 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 270 " --> pdb=" O ALA A 285 " (cutoff:3.500A) 1099 hydrogen bonds defined for protein. 3189 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: 5.04 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9033 1.34 - 1.46: 6295 1.46 - 1.58: 13375 1.58 - 1.70: 0 1.70 - 1.83: 116 Bond restraints: 28819 Sorted by residual: bond pdb=" N LEU B1009 " pdb=" CA LEU B1009 " ideal model delta sigma weight residual 1.458 1.505 -0.047 1.90e-02 2.77e+03 6.02e+00 bond pdb=" C ASP D 314 " pdb=" N PRO D 315 " ideal model delta sigma weight residual 1.334 1.388 -0.055 2.34e-02 1.83e+03 5.43e+00 bond pdb=" C ASP E 314 " pdb=" N PRO E 315 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.40e+00 bond pdb=" C ASN C1010 " pdb=" N PRO C1011 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.72e+00 bond pdb=" C THR D 201 " pdb=" N PRO D 202 " ideal model delta sigma weight residual 1.331 1.357 -0.025 1.21e-02 6.83e+03 4.37e+00 ... (remaining 28814 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 38457 3.58 - 7.16: 411 7.16 - 10.74: 66 10.74 - 14.32: 7 14.32 - 17.89: 3 Bond angle restraints: 38944 Sorted by residual: angle pdb=" C PRO B1008 " pdb=" N LEU B1009 " pdb=" CA LEU B1009 " ideal model delta sigma weight residual 121.70 134.68 -12.98 1.80e+00 3.09e-01 5.20e+01 angle pdb=" C GLY A 374 " pdb=" N LEU A 375 " pdb=" CA LEU A 375 " ideal model delta sigma weight residual 120.06 128.16 -8.10 1.19e+00 7.06e-01 4.63e+01 angle pdb=" C GLU B 860 " pdb=" N LYS B 861 " pdb=" CA LYS B 861 " ideal model delta sigma weight residual 121.70 133.42 -11.72 1.80e+00 3.09e-01 4.24e+01 angle pdb=" C GLU E 420 " pdb=" N LEU E 421 " pdb=" CA LEU E 421 " ideal model delta sigma weight residual 121.70 132.22 -10.52 1.80e+00 3.09e-01 3.42e+01 angle pdb=" C LEU B1003 " pdb=" N PRO B1004 " pdb=" CD PRO B1004 " ideal model delta sigma weight residual 120.60 107.87 12.73 2.20e+00 2.07e-01 3.35e+01 ... (remaining 38939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 16262 16.10 - 32.21: 857 32.21 - 48.31: 205 48.31 - 64.41: 10 64.41 - 80.52: 25 Dihedral angle restraints: 17359 sinusoidal: 7002 harmonic: 10357 Sorted by residual: dihedral pdb=" CA VAL E 474 " pdb=" C VAL E 474 " pdb=" N GLU E 475 " pdb=" CA GLU E 475 " ideal model delta harmonic sigma weight residual 180.00 137.51 42.49 0 5.00e+00 4.00e-02 7.22e+01 dihedral pdb=" CA ARG C 678 " pdb=" C ARG C 678 " pdb=" N TYR C 679 " pdb=" CA TYR C 679 " ideal model delta harmonic sigma weight residual -180.00 -140.44 -39.56 0 5.00e+00 4.00e-02 6.26e+01 dihedral pdb=" CA TYR E 274 " pdb=" C TYR E 274 " pdb=" N ASP E 275 " pdb=" CA ASP E 275 " ideal model delta harmonic sigma weight residual -180.00 -142.84 -37.16 0 5.00e+00 4.00e-02 5.52e+01 ... (remaining 17356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3627 0.076 - 0.151: 611 0.151 - 0.227: 57 0.227 - 0.303: 10 0.303 - 0.379: 2 Chirality restraints: 4307 Sorted by residual: chirality pdb=" CB ILE D 79 " pdb=" CA ILE D 79 " pdb=" CG1 ILE D 79 " pdb=" CG2 ILE D 79 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CB VAL A 35 " pdb=" CA VAL A 35 " pdb=" CG1 VAL A 35 " pdb=" CG2 VAL A 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB VAL D 27 " pdb=" CA VAL D 27 " pdb=" CG1 VAL D 27 " pdb=" CG2 VAL D 27 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 4304 not shown) Planarity restraints: 5056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 302 " 0.058 5.00e-02 4.00e+02 8.76e-02 1.23e+01 pdb=" N PRO E 303 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO E 303 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 303 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 17 " 0.032 2.00e-02 2.50e+03 2.19e-02 1.20e+01 pdb=" CG TRP E 17 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP E 17 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP E 17 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 17 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 17 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 17 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 17 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 17 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 17 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 117 " 0.027 2.00e-02 2.50e+03 2.18e-02 1.19e+01 pdb=" CG TRP A 117 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 117 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 117 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 117 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 117 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 117 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 117 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 117 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 117 " -0.002 2.00e-02 2.50e+03 ... (remaining 5053 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4717 2.77 - 3.30: 27085 3.30 - 3.83: 46837 3.83 - 4.37: 54373 4.37 - 4.90: 88716 Nonbonded interactions: 221728 Sorted by model distance: nonbonded pdb=" O GLY E 131 " pdb=" OH TYR E 274 " model vdw 2.232 3.040 nonbonded pdb=" O ILE B 713 " pdb=" OG1 THR B 717 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR E 411 " pdb=" O VAL E 456 " model vdw 2.277 3.040 nonbonded pdb=" OG SER C 581 " pdb=" O THR C 598 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR G 7 " pdb=" OD2 ASP G 92 " model vdw 2.287 3.040 ... (remaining 221723 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 'B' and (resid 30 through 180 or resid 191 through 861 or resid 872 throu \ gh 1035)) selection = (chain 'C' and (resid 30 through 584 or resid 591 through 1035)) } ncs_group { reference = (chain 'D' and (resid 10 through 422 or (resid 423 and (name N or name CA or nam \ e C or name O or name CB )) or resid 424 through 510)) selection = (chain 'E' and (resid 10 through 55 or resid 72 through 510)) } ncs_group { reference = chain 'F' selection = chain 'G' } 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 group one per residue 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.020 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28819 Z= 0.226 Angle : 1.029 17.895 38944 Z= 0.563 Chirality : 0.056 0.379 4307 Planarity : 0.007 0.088 5056 Dihedral : 11.111 80.515 10637 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 0.56 % Allowed : 4.01 % Favored : 95.43 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 2.17 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.41 (0.11), residues: 3464 helix: -2.73 (0.10), residues: 1505 sheet: -2.27 (0.29), residues: 264 loop : -3.23 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 483 TYR 0.056 0.003 TYR B 846 PHE 0.030 0.003 PHE C 954 TRP 0.058 0.003 TRP E 17 HIS 0.014 0.002 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00449 (28819) covalent geometry : angle 1.02946 (38944) hydrogen bonds : bond 0.15097 ( 1092) hydrogen bonds : angle 7.45099 ( 3189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 432 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 MET cc_start: 0.7190 (mmm) cc_final: 0.6743 (mmm) REVERT: B 390 MET cc_start: 0.7724 (mtm) cc_final: 0.7479 (mtt) REVERT: B 786 LEU cc_start: 0.9440 (mt) cc_final: 0.9214 (tt) REVERT: B 997 THR cc_start: 0.8549 (p) cc_final: 0.8326 (t) REVERT: C 155 LEU cc_start: 0.9278 (mt) cc_final: 0.8910 (mt) REVERT: C 335 PHE cc_start: 0.7848 (t80) cc_final: 0.7358 (t80) REVERT: C 652 LEU cc_start: 0.9093 (tp) cc_final: 0.8655 (mp) REVERT: C 737 MET cc_start: 0.8127 (mmm) cc_final: 0.7890 (mmm) REVERT: C 752 PHE cc_start: 0.8232 (t80) cc_final: 0.7224 (t80) REVERT: D 206 SER cc_start: 0.9316 (m) cc_final: 0.8694 (p) REVERT: E 157 VAL cc_start: 0.7409 (t) cc_final: 0.7177 (p) REVERT: E 291 ARG cc_start: 0.7788 (mpp80) cc_final: 0.7434 (tpm170) REVERT: E 319 ASN cc_start: 0.8312 (t0) cc_final: 0.7507 (p0) REVERT: E 431 LEU cc_start: 0.7693 (mt) cc_final: 0.7411 (mp) REVERT: F 21 ASN cc_start: 0.8928 (m-40) cc_final: 0.7903 (p0) REVERT: F 87 GLU cc_start: 0.9065 (tt0) cc_final: 0.8648 (tp30) REVERT: F 89 LEU cc_start: 0.9465 (mt) cc_final: 0.8974 (pp) REVERT: G 17 MET cc_start: 0.8610 (mtp) cc_final: 0.8372 (mtt) REVERT: G 21 ASN cc_start: 0.8396 (m-40) cc_final: 0.7811 (p0) REVERT: G 65 PHE cc_start: 0.7329 (m-10) cc_final: 0.6531 (m-10) REVERT: A 100 MET cc_start: 0.5845 (mmm) cc_final: 0.5275 (tmm) REVERT: A 217 THR cc_start: 0.4746 (m) cc_final: 0.4019 (t) REVERT: A 380 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6646 (pp20) outliers start: 17 outliers final: 2 residues processed: 448 average time/residue: 0.2186 time to fit residues: 147.6790 Evaluate side-chains 199 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 196 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN B 91 ASN B 199 GLN ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 514 GLN B 561 GLN B 622 HIS B 648 GLN B 857 GLN B 924 ASN ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 91 ASN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS C 529 HIS C 622 HIS C 635 GLN C 701 ASN C 726 ASN C 958 GLN D 21 ASN D 90 GLN ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 ASN D 412 ASN D 427 ASN D 489 ASN E 18 GLN E 21 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN E 211 GLN E 379 ASN E 435 HIS ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN A 313 HIS ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.078748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.060370 restraints weight = 190008.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.061387 restraints weight = 122903.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.061358 restraints weight = 89650.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.061848 restraints weight = 74033.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.061841 restraints weight = 64470.575| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 28819 Z= 0.181 Angle : 0.738 16.186 38944 Z= 0.391 Chirality : 0.046 0.213 4307 Planarity : 0.005 0.070 5056 Dihedral : 7.056 38.681 3789 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.13 % Allowed : 2.56 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.13), residues: 3464 helix: -1.25 (0.12), residues: 1538 sheet: -1.89 (0.29), residues: 310 loop : -2.98 (0.14), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 264 TYR 0.027 0.002 TYR D 260 PHE 0.043 0.002 PHE D 277 TRP 0.027 0.002 TRP A 117 HIS 0.009 0.001 HIS F 34 Details of bonding type rmsd covalent geometry : bond 0.00380 (28819) covalent geometry : angle 0.73834 (38944) hydrogen bonds : bond 0.04367 ( 1092) hydrogen bonds : angle 5.40635 ( 3189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 252 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 MET cc_start: 0.8313 (mmm) cc_final: 0.7700 (mmm) REVERT: B 356 ASP cc_start: 0.6095 (m-30) cc_final: 0.5823 (t70) REVERT: B 390 MET cc_start: 0.7475 (mtm) cc_final: 0.7270 (ptm) REVERT: B 422 LEU cc_start: 0.8963 (tt) cc_final: 0.8698 (mt) REVERT: B 658 MET cc_start: 0.2616 (mmp) cc_final: 0.2294 (mmp) REVERT: B 686 PHE cc_start: 0.9053 (m-10) cc_final: 0.8609 (m-80) REVERT: C 44 LEU cc_start: 0.8752 (mt) cc_final: 0.8526 (mt) REVERT: C 155 LEU cc_start: 0.9248 (mt) cc_final: 0.8891 (mt) REVERT: C 227 MET cc_start: 0.7231 (mmp) cc_final: 0.6733 (mmm) REVERT: C 335 PHE cc_start: 0.8192 (t80) cc_final: 0.7826 (t80) REVERT: C 348 LYS cc_start: 0.9262 (mmpt) cc_final: 0.8554 (mmmt) REVERT: C 390 MET cc_start: 0.8170 (tpp) cc_final: 0.7748 (tpp) REVERT: C 653 LEU cc_start: 0.8940 (tt) cc_final: 0.8601 (tt) REVERT: D 93 CYS cc_start: 0.6553 (t) cc_final: 0.6290 (t) REVERT: D 265 MET cc_start: 0.8470 (ptp) cc_final: 0.8238 (ptm) REVERT: D 393 PHE cc_start: 0.5917 (t80) cc_final: 0.5511 (t80) REVERT: E 291 ARG cc_start: 0.8555 (mpp80) cc_final: 0.7683 (tpm170) REVERT: E 319 ASN cc_start: 0.8319 (t0) cc_final: 0.7881 (m-40) REVERT: E 431 LEU cc_start: 0.7817 (mt) cc_final: 0.7495 (mp) REVERT: F 21 ASN cc_start: 0.8721 (m-40) cc_final: 0.7969 (p0) REVERT: F 71 MET cc_start: 0.6425 (ptt) cc_final: 0.5909 (ppp) REVERT: G 5 MET cc_start: 0.7488 (ttm) cc_final: 0.7258 (ttm) REVERT: G 17 MET cc_start: 0.8626 (mtp) cc_final: 0.8258 (mtt) REVERT: G 65 PHE cc_start: 0.6430 (m-10) cc_final: 0.6141 (m-10) REVERT: A 98 MET cc_start: -0.2459 (ttm) cc_final: -0.2895 (ttm) REVERT: A 100 MET cc_start: 0.6311 (mmm) cc_final: 0.5554 (tmm) REVERT: A 239 MET cc_start: 0.4295 (mtt) cc_final: 0.3960 (ppp) outliers start: 4 outliers final: 0 residues processed: 255 average time/residue: 0.1929 time to fit residues: 78.7410 Evaluate side-chains 154 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 212 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 317 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 191 optimal weight: 0.9990 chunk 147 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 233 optimal weight: 0.3980 chunk 303 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 GLN ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN C 419 GLN ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 GLN C 886 GLN D 261 ASN ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN E 90 GLN E 102 ASN E 379 ASN F 21 ASN ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.079099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.059044 restraints weight = 188767.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.060250 restraints weight = 118735.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.061155 restraints weight = 86750.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.061591 restraints weight = 70803.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.062005 restraints weight = 62816.545| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28819 Z= 0.132 Angle : 0.665 16.062 38944 Z= 0.350 Chirality : 0.045 0.204 4307 Planarity : 0.005 0.065 5056 Dihedral : 6.436 35.028 3789 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.10 % Allowed : 3.06 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.14), residues: 3464 helix: -0.51 (0.13), residues: 1527 sheet: -1.65 (0.29), residues: 312 loop : -2.82 (0.14), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 710 TYR 0.038 0.002 TYR D 260 PHE 0.030 0.001 PHE D 277 TRP 0.045 0.002 TRP E 17 HIS 0.007 0.001 HIS F 34 Details of bonding type rmsd covalent geometry : bond 0.00275 (28819) covalent geometry : angle 0.66512 (38944) hydrogen bonds : bond 0.03937 ( 1092) hydrogen bonds : angle 4.94814 ( 3189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 225 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 MET cc_start: 0.8818 (mpp) cc_final: 0.8247 (mmt) REVERT: B 130 MET cc_start: 0.8380 (mmm) cc_final: 0.7666 (mmm) REVERT: B 422 LEU cc_start: 0.9149 (tt) cc_final: 0.8854 (mt) REVERT: B 686 PHE cc_start: 0.9065 (m-10) cc_final: 0.8659 (m-80) REVERT: C 155 LEU cc_start: 0.9359 (mt) cc_final: 0.8938 (mt) REVERT: C 348 LYS cc_start: 0.9224 (mmpt) cc_final: 0.8810 (mmmt) REVERT: C 542 LEU cc_start: 0.9216 (mt) cc_final: 0.8837 (mt) REVERT: C 722 LYS cc_start: 0.8191 (mttt) cc_final: 0.7971 (mmtm) REVERT: C 974 LEU cc_start: 0.6793 (tp) cc_final: 0.6542 (mm) REVERT: E 291 ARG cc_start: 0.8564 (mpp80) cc_final: 0.7770 (tpm170) REVERT: E 412 ASN cc_start: 0.9020 (m-40) cc_final: 0.8605 (p0) REVERT: E 431 LEU cc_start: 0.7722 (mt) cc_final: 0.7404 (pt) REVERT: F 17 MET cc_start: 0.7109 (ttm) cc_final: 0.6810 (ttm) REVERT: G 17 MET cc_start: 0.8608 (mtp) cc_final: 0.8248 (mtt) REVERT: G 65 PHE cc_start: 0.6877 (m-10) cc_final: 0.6598 (m-80) REVERT: A 100 MET cc_start: 0.6138 (mmm) cc_final: 0.5635 (tmm) outliers start: 3 outliers final: 0 residues processed: 228 average time/residue: 0.1952 time to fit residues: 71.5338 Evaluate side-chains 148 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 261 optimal weight: 9.9990 chunk 219 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 346 optimal weight: 0.9990 chunk 290 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 GLN ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 GLN ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 GLN ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 379 ASN ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.079377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.059353 restraints weight = 189546.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.060451 restraints weight = 120401.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.061283 restraints weight = 89799.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.061989 restraints weight = 73765.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.062338 restraints weight = 64450.013| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28819 Z= 0.121 Angle : 0.639 15.632 38944 Z= 0.334 Chirality : 0.044 0.237 4307 Planarity : 0.004 0.062 5056 Dihedral : 6.050 35.143 3789 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.07 % Allowed : 2.60 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.14), residues: 3464 helix: -0.13 (0.13), residues: 1513 sheet: -1.52 (0.29), residues: 327 loop : -2.67 (0.14), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 14 TYR 0.029 0.001 TYR D 123 PHE 0.023 0.001 PHE C 223 TRP 0.017 0.001 TRP F 94 HIS 0.006 0.001 HIS F 34 Details of bonding type rmsd covalent geometry : bond 0.00257 (28819) covalent geometry : angle 0.63935 (38944) hydrogen bonds : bond 0.03638 ( 1092) hydrogen bonds : angle 4.71867 ( 3189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 MET cc_start: 0.8757 (mpp) cc_final: 0.8160 (mmt) REVERT: B 130 MET cc_start: 0.8333 (mmm) cc_final: 0.7630 (mmm) REVERT: B 347 MET cc_start: 0.5301 (mpp) cc_final: 0.5074 (mpp) REVERT: B 604 MET cc_start: -0.0287 (ttt) cc_final: -0.0632 (mtp) REVERT: B 686 PHE cc_start: 0.9110 (m-10) cc_final: 0.8825 (m-80) REVERT: B 753 MET cc_start: 0.8621 (mmm) cc_final: 0.8203 (mmm) REVERT: C 44 LEU cc_start: 0.8932 (mt) cc_final: 0.8714 (mt) REVERT: C 335 PHE cc_start: 0.8177 (t80) cc_final: 0.7818 (t80) REVERT: C 347 MET cc_start: 0.9342 (tmm) cc_final: 0.8991 (tmm) REVERT: C 348 LYS cc_start: 0.9254 (mmpt) cc_final: 0.8914 (mmmt) REVERT: C 542 LEU cc_start: 0.9197 (mt) cc_final: 0.8330 (mp) REVERT: C 722 LYS cc_start: 0.8331 (mttt) cc_final: 0.8034 (mmtm) REVERT: C 792 LEU cc_start: 0.9642 (mt) cc_final: 0.9390 (mt) REVERT: C 910 MET cc_start: 0.7401 (mmp) cc_final: 0.6732 (mmm) REVERT: C 1029 GLU cc_start: 0.8742 (tp30) cc_final: 0.8460 (tp30) REVERT: D 139 THR cc_start: 0.8855 (p) cc_final: 0.8542 (t) REVERT: D 265 MET cc_start: 0.8615 (ptp) cc_final: 0.8393 (ptm) REVERT: D 393 PHE cc_start: 0.6028 (t80) cc_final: 0.5696 (t80) REVERT: E 291 ARG cc_start: 0.8546 (mpp80) cc_final: 0.7657 (tpm170) REVERT: E 319 ASN cc_start: 0.8112 (m-40) cc_final: 0.7898 (m-40) REVERT: E 412 ASN cc_start: 0.8983 (m-40) cc_final: 0.8648 (p0) REVERT: E 431 LEU cc_start: 0.7729 (mt) cc_final: 0.7400 (pt) REVERT: F 15 TYR cc_start: 0.8941 (t80) cc_final: 0.8690 (t80) REVERT: F 17 MET cc_start: 0.7182 (ttm) cc_final: 0.6880 (ttm) REVERT: F 87 GLU cc_start: 0.9414 (tp30) cc_final: 0.9178 (tp30) REVERT: F 93 LEU cc_start: 0.8683 (mt) cc_final: 0.8473 (mt) REVERT: G 17 MET cc_start: 0.8613 (mtp) cc_final: 0.8307 (mtt) REVERT: G 51 ASP cc_start: 0.8219 (m-30) cc_final: 0.7915 (m-30) REVERT: A 100 MET cc_start: 0.6136 (mmm) cc_final: 0.5823 (tmm) REVERT: A 380 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7327 (pt0) outliers start: 2 outliers final: 0 residues processed: 221 average time/residue: 0.1649 time to fit residues: 60.3140 Evaluate side-chains 149 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 6 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 177 optimal weight: 0.4980 chunk 180 optimal weight: 9.9990 chunk 193 optimal weight: 30.0000 chunk 338 optimal weight: 6.9990 chunk 318 optimal weight: 30.0000 chunk 323 optimal weight: 9.9990 chunk 271 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 GLN B 431 GLN B 833 GLN ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN C 370 ASN C 561 GLN ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 HIS D 102 ASN D 215 HIS D 289 HIS ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 HIS E 102 ASN E 379 ASN E 451 HIS ** G 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 GLN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.076804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.058512 restraints weight = 192727.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.059413 restraints weight = 131453.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.059231 restraints weight = 103636.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.059835 restraints weight = 86416.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.059717 restraints weight = 75844.501| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28819 Z= 0.215 Angle : 0.731 14.497 38944 Z= 0.383 Chirality : 0.046 0.233 4307 Planarity : 0.005 0.065 5056 Dihedral : 6.295 34.387 3789 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 0.03 % Allowed : 2.33 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.14), residues: 3464 helix: -0.18 (0.13), residues: 1519 sheet: -1.45 (0.29), residues: 331 loop : -2.68 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 710 TYR 0.023 0.002 TYR B 30 PHE 0.030 0.002 PHE D 415 TRP 0.020 0.002 TRP F 94 HIS 0.006 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00451 (28819) covalent geometry : angle 0.73054 (38944) hydrogen bonds : bond 0.04046 ( 1092) hydrogen bonds : angle 4.98551 ( 3189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 MET cc_start: 0.8445 (mmm) cc_final: 0.7702 (mmm) REVERT: B 604 MET cc_start: 0.0670 (ttt) cc_final: -0.0388 (ttt) REVERT: B 686 PHE cc_start: 0.9178 (m-10) cc_final: 0.8909 (m-80) REVERT: C 335 PHE cc_start: 0.8404 (t80) cc_final: 0.8005 (t80) REVERT: C 344 TYR cc_start: 0.7909 (t80) cc_final: 0.7420 (t80) REVERT: C 347 MET cc_start: 0.9381 (tmm) cc_final: 0.8808 (tmm) REVERT: C 348 LYS cc_start: 0.9228 (mmpt) cc_final: 0.8861 (mmmt) REVERT: C 542 LEU cc_start: 0.9275 (mt) cc_final: 0.8822 (mt) REVERT: C 653 LEU cc_start: 0.8872 (tp) cc_final: 0.8666 (tt) REVERT: C 722 LYS cc_start: 0.8417 (mttt) cc_final: 0.8072 (mmtm) REVERT: C 910 MET cc_start: 0.7553 (mmp) cc_final: 0.6760 (mmm) REVERT: D 123 TYR cc_start: 0.5927 (p90) cc_final: 0.5720 (p90) REVERT: D 139 THR cc_start: 0.8914 (p) cc_final: 0.8571 (t) REVERT: D 393 PHE cc_start: 0.6123 (t80) cc_final: 0.5697 (t80) REVERT: E 265 MET cc_start: 0.9012 (pmm) cc_final: 0.8255 (pmm) REVERT: E 291 ARG cc_start: 0.8671 (mpp80) cc_final: 0.7656 (tpm170) REVERT: F 17 MET cc_start: 0.7268 (ttm) cc_final: 0.6885 (ttm) REVERT: F 87 GLU cc_start: 0.9373 (tp30) cc_final: 0.9093 (tp30) REVERT: G 17 MET cc_start: 0.8670 (mtp) cc_final: 0.8410 (mtt) REVERT: G 51 ASP cc_start: 0.8264 (m-30) cc_final: 0.8001 (m-30) REVERT: G 65 PHE cc_start: 0.6718 (m-10) cc_final: 0.6248 (m-10) REVERT: G 78 ILE cc_start: 0.9301 (tt) cc_final: 0.9053 (mm) REVERT: A 100 MET cc_start: 0.6518 (mmm) cc_final: 0.5641 (tmm) REVERT: A 239 MET cc_start: 0.4738 (ptt) cc_final: 0.4117 (ptt) outliers start: 1 outliers final: 1 residues processed: 180 average time/residue: 0.1683 time to fit residues: 50.7666 Evaluate side-chains 131 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 277 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 213 optimal weight: 1.9990 chunk 252 optimal weight: 0.2980 chunk 237 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 234 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 GLN B 622 HIS ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN C 370 ASN C 561 GLN C 588 GLN D 102 ASN D 373 GLN ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 379 ASN G 34 HIS ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.078787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.060481 restraints weight = 188934.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.061538 restraints weight = 129174.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.061409 restraints weight = 96130.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.061796 restraints weight = 80428.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.061864 restraints weight = 71592.910| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28819 Z= 0.118 Angle : 0.637 14.928 38944 Z= 0.330 Chirality : 0.044 0.222 4307 Planarity : 0.004 0.060 5056 Dihedral : 5.891 36.704 3789 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.07 % Allowed : 2.01 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.14), residues: 3464 helix: 0.11 (0.14), residues: 1505 sheet: -1.52 (0.29), residues: 329 loop : -2.55 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 14 TYR 0.016 0.001 TYR C 49 PHE 0.019 0.001 PHE D 415 TRP 0.044 0.001 TRP E 17 HIS 0.007 0.001 HIS B 622 Details of bonding type rmsd covalent geometry : bond 0.00248 (28819) covalent geometry : angle 0.63666 (38944) hydrogen bonds : bond 0.03562 ( 1092) hydrogen bonds : angle 4.64031 ( 3189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8493 (m-80) cc_final: 0.8263 (m-10) REVERT: B 130 MET cc_start: 0.8134 (mmm) cc_final: 0.7508 (mmm) REVERT: B 422 LEU cc_start: 0.9015 (mm) cc_final: 0.8812 (mm) REVERT: B 604 MET cc_start: 0.0367 (ttt) cc_final: -0.0498 (ttt) REVERT: B 686 PHE cc_start: 0.9181 (m-10) cc_final: 0.8834 (m-80) REVERT: B 753 MET cc_start: 0.8391 (mmm) cc_final: 0.7854 (mmm) REVERT: C 335 PHE cc_start: 0.8425 (t80) cc_final: 0.7977 (t80) REVERT: C 347 MET cc_start: 0.9371 (tmm) cc_final: 0.9137 (tmm) REVERT: C 348 LYS cc_start: 0.9213 (mmpt) cc_final: 0.8898 (mmmt) REVERT: C 653 LEU cc_start: 0.8805 (tp) cc_final: 0.8587 (tt) REVERT: C 722 LYS cc_start: 0.8307 (mttt) cc_final: 0.7973 (mmtm) REVERT: C 910 MET cc_start: 0.7304 (mmp) cc_final: 0.7070 (mmm) REVERT: C 1029 GLU cc_start: 0.8812 (tp30) cc_final: 0.8580 (tp30) REVERT: D 139 THR cc_start: 0.8805 (p) cc_final: 0.8518 (t) REVERT: D 275 ASP cc_start: 0.7049 (p0) cc_final: 0.6640 (p0) REVERT: D 373 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8325 (tm-30) REVERT: E 265 MET cc_start: 0.9141 (pmm) cc_final: 0.8325 (pmm) REVERT: E 291 ARG cc_start: 0.8536 (mpp80) cc_final: 0.7568 (tpm170) REVERT: E 412 ASN cc_start: 0.8866 (m-40) cc_final: 0.8497 (p0) REVERT: F 17 MET cc_start: 0.7189 (ttm) cc_final: 0.6811 (ttm) REVERT: G 17 MET cc_start: 0.8799 (mtp) cc_final: 0.8516 (mtt) REVERT: G 51 ASP cc_start: 0.8069 (m-30) cc_final: 0.7773 (m-30) REVERT: G 78 ILE cc_start: 0.9304 (tt) cc_final: 0.9100 (mm) REVERT: A 100 MET cc_start: 0.6375 (mmm) cc_final: 0.5889 (tmm) REVERT: A 181 MET cc_start: 0.7478 (mmm) cc_final: 0.7254 (mmm) REVERT: A 239 MET cc_start: 0.4936 (ptt) cc_final: 0.4286 (ptt) outliers start: 2 outliers final: 1 residues processed: 193 average time/residue: 0.1731 time to fit residues: 55.9315 Evaluate side-chains 134 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 158 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 246 optimal weight: 9.9990 chunk 290 optimal weight: 1.9990 chunk 201 optimal weight: 0.4980 chunk 112 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 208 optimal weight: 0.4980 chunk 327 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 GLN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 HIS ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN C 561 GLN D 102 ASN ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 379 ASN ** A 84 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 = 0.3845 r_free = 0.3845 target = 0.078875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.060421 restraints weight = 187700.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.061361 restraints weight = 124987.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.061231 restraints weight = 99552.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.061673 restraints weight = 80456.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.061913 restraints weight = 69490.535| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28819 Z= 0.118 Angle : 0.642 14.891 38944 Z= 0.331 Chirality : 0.044 0.218 4307 Planarity : 0.004 0.062 5056 Dihedral : 5.675 34.909 3789 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.03 % Allowed : 1.35 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.14), residues: 3464 helix: 0.27 (0.14), residues: 1503 sheet: -1.48 (0.29), residues: 333 loop : -2.45 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 14 TYR 0.015 0.001 TYR E 260 PHE 0.016 0.001 PHE C 557 TRP 0.019 0.001 TRP F 94 HIS 0.006 0.001 HIS D 244 Details of bonding type rmsd covalent geometry : bond 0.00252 (28819) covalent geometry : angle 0.64169 (38944) hydrogen bonds : bond 0.03481 ( 1092) hydrogen bonds : angle 4.55538 ( 3189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8534 (m-80) cc_final: 0.8200 (m-10) REVERT: B 130 MET cc_start: 0.8160 (mmm) cc_final: 0.7499 (mmm) REVERT: B 422 LEU cc_start: 0.9072 (mm) cc_final: 0.8625 (mt) REVERT: B 604 MET cc_start: 0.0260 (ttt) cc_final: -0.0374 (ttt) REVERT: B 686 PHE cc_start: 0.9164 (m-10) cc_final: 0.8898 (m-80) REVERT: C 335 PHE cc_start: 0.8433 (t80) cc_final: 0.7966 (t80) REVERT: C 347 MET cc_start: 0.9371 (tmm) cc_final: 0.8968 (tmm) REVERT: C 653 LEU cc_start: 0.8735 (tp) cc_final: 0.8513 (tt) REVERT: C 722 LYS cc_start: 0.8261 (mttt) cc_final: 0.7951 (mmtm) REVERT: C 1029 GLU cc_start: 0.8750 (tp30) cc_final: 0.8491 (tp30) REVERT: D 123 TYR cc_start: 0.5464 (p90) cc_final: 0.5224 (p90) REVERT: D 139 THR cc_start: 0.8860 (p) cc_final: 0.8568 (t) REVERT: D 275 ASP cc_start: 0.7197 (p0) cc_final: 0.6760 (p0) REVERT: D 393 PHE cc_start: 0.6153 (t80) cc_final: 0.5937 (t80) REVERT: E 265 MET cc_start: 0.9108 (pmm) cc_final: 0.8356 (pmm) REVERT: E 291 ARG cc_start: 0.8530 (mpp80) cc_final: 0.7613 (tpm170) REVERT: E 412 ASN cc_start: 0.8808 (m-40) cc_final: 0.8495 (p0) REVERT: F 17 MET cc_start: 0.7221 (ttm) cc_final: 0.6828 (ttm) REVERT: G 17 MET cc_start: 0.8763 (mtp) cc_final: 0.8467 (mtt) REVERT: G 51 ASP cc_start: 0.8002 (m-30) cc_final: 0.7788 (m-30) REVERT: A 100 MET cc_start: 0.6368 (mmm) cc_final: 0.5738 (tmm) REVERT: A 239 MET cc_start: 0.5053 (ptt) cc_final: 0.4394 (ptt) outliers start: 1 outliers final: 1 residues processed: 188 average time/residue: 0.1814 time to fit residues: 56.2325 Evaluate side-chains 131 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 141 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 200 optimal weight: 0.1980 chunk 150 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 287 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 94 optimal weight: 0.0970 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN B 431 GLN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN C 561 GLN C 680 HIS D 102 ASN ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 ASN E 102 ASN E 379 ASN F 13 HIS ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.079150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.061073 restraints weight = 189484.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.062067 restraints weight = 125844.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.061979 restraints weight = 92995.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.062466 restraints weight = 76461.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.062471 restraints weight = 68596.972| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28819 Z= 0.116 Angle : 0.637 14.904 38944 Z= 0.327 Chirality : 0.043 0.217 4307 Planarity : 0.004 0.061 5056 Dihedral : 5.559 34.438 3789 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.03 % Allowed : 0.99 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 3464 helix: 0.33 (0.14), residues: 1519 sheet: -1.42 (0.29), residues: 333 loop : -2.44 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 14 TYR 0.019 0.001 TYR C 344 PHE 0.017 0.001 PHE D 415 TRP 0.017 0.001 TRP F 94 HIS 0.005 0.001 HIS D 244 Details of bonding type rmsd covalent geometry : bond 0.00250 (28819) covalent geometry : angle 0.63693 (38944) hydrogen bonds : bond 0.03417 ( 1092) hydrogen bonds : angle 4.51463 ( 3189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8490 (m-80) cc_final: 0.8153 (m-10) REVERT: B 130 MET cc_start: 0.8192 (mmm) cc_final: 0.7513 (mmm) REVERT: B 352 ARG cc_start: 0.5652 (ptt-90) cc_final: 0.5323 (ptt-90) REVERT: B 422 LEU cc_start: 0.9105 (mm) cc_final: 0.8629 (mt) REVERT: B 604 MET cc_start: 0.0167 (ttt) cc_final: -0.0515 (ttt) REVERT: B 686 PHE cc_start: 0.9175 (m-10) cc_final: 0.8876 (m-80) REVERT: B 753 MET cc_start: 0.8349 (mmm) cc_final: 0.7837 (mmm) REVERT: C 335 PHE cc_start: 0.8393 (t80) cc_final: 0.7961 (t80) REVERT: C 347 MET cc_start: 0.9368 (tmm) cc_final: 0.9153 (tmm) REVERT: C 348 LYS cc_start: 0.9235 (mmpt) cc_final: 0.8885 (mmmt) REVERT: C 390 MET cc_start: 0.7714 (tpt) cc_final: 0.7148 (tpp) REVERT: C 722 LYS cc_start: 0.8259 (mttt) cc_final: 0.7900 (mmtm) REVERT: C 1029 GLU cc_start: 0.8827 (tp30) cc_final: 0.8515 (tp30) REVERT: D 123 TYR cc_start: 0.5394 (p90) cc_final: 0.5182 (p90) REVERT: D 139 THR cc_start: 0.8939 (p) cc_final: 0.8667 (t) REVERT: D 275 ASP cc_start: 0.7011 (p0) cc_final: 0.6584 (p0) REVERT: D 477 LYS cc_start: 0.7867 (pttt) cc_final: 0.7345 (tptt) REVERT: E 291 ARG cc_start: 0.8516 (mpp80) cc_final: 0.7623 (tpm170) REVERT: E 412 ASN cc_start: 0.8796 (m-40) cc_final: 0.8451 (p0) REVERT: F 17 MET cc_start: 0.7293 (ttm) cc_final: 0.7039 (ttm) REVERT: G 17 MET cc_start: 0.8770 (mtp) cc_final: 0.8519 (mtt) REVERT: G 51 ASP cc_start: 0.7963 (m-30) cc_final: 0.7666 (m-30) REVERT: A 100 MET cc_start: 0.6376 (mmm) cc_final: 0.5755 (tmm) REVERT: A 239 MET cc_start: 0.5025 (ptt) cc_final: 0.4348 (ptt) outliers start: 1 outliers final: 1 residues processed: 182 average time/residue: 0.1763 time to fit residues: 53.3719 Evaluate side-chains 136 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 144 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 253 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 290 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 317 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 chunk 346 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 GLN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN C 526 GLN C 561 GLN C 680 HIS D 102 ASN ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 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 = 0.3845 r_free = 0.3845 target = 0.078890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.059341 restraints weight = 189389.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.060429 restraints weight = 121385.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.061321 restraints weight = 89910.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.061848 restraints weight = 74333.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.062087 restraints weight = 66085.951| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28819 Z= 0.122 Angle : 0.638 14.686 38944 Z= 0.326 Chirality : 0.043 0.217 4307 Planarity : 0.004 0.061 5056 Dihedral : 5.455 33.157 3789 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.03 % Allowed : 0.72 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.14), residues: 3464 helix: 0.43 (0.14), residues: 1513 sheet: -1.25 (0.29), residues: 345 loop : -2.47 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 14 TYR 0.032 0.001 TYR C 553 PHE 0.015 0.001 PHE D 277 TRP 0.019 0.001 TRP F 94 HIS 0.007 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00261 (28819) covalent geometry : angle 0.63758 (38944) hydrogen bonds : bond 0.03377 ( 1092) hydrogen bonds : angle 4.46653 ( 3189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8447 (m-80) cc_final: 0.8057 (m-10) REVERT: B 60 MET cc_start: 0.8878 (mpp) cc_final: 0.8562 (mpp) REVERT: B 130 MET cc_start: 0.8275 (mmm) cc_final: 0.7587 (mmm) REVERT: B 208 ASP cc_start: 0.8024 (p0) cc_final: 0.7792 (p0) REVERT: B 352 ARG cc_start: 0.5897 (ptt-90) cc_final: 0.5542 (ptt-90) REVERT: B 422 LEU cc_start: 0.9112 (mm) cc_final: 0.8645 (mt) REVERT: B 604 MET cc_start: -0.0962 (ttt) cc_final: -0.1658 (ttt) REVERT: B 686 PHE cc_start: 0.9115 (m-10) cc_final: 0.8876 (m-80) REVERT: B 753 MET cc_start: 0.8286 (mmm) cc_final: 0.7774 (mmm) REVERT: C 335 PHE cc_start: 0.8446 (t80) cc_final: 0.7994 (t80) REVERT: C 347 MET cc_start: 0.9406 (tmm) cc_final: 0.9140 (tmm) REVERT: C 348 LYS cc_start: 0.9245 (mmpt) cc_final: 0.8859 (mmmt) REVERT: C 390 MET cc_start: 0.7640 (tpt) cc_final: 0.7057 (tpp) REVERT: C 653 LEU cc_start: 0.8952 (tp) cc_final: 0.8743 (tt) REVERT: C 722 LYS cc_start: 0.8299 (mttt) cc_final: 0.7967 (mmtm) REVERT: C 1029 GLU cc_start: 0.8876 (tp30) cc_final: 0.8571 (tp30) REVERT: D 123 TYR cc_start: 0.5485 (p90) cc_final: 0.5216 (p90) REVERT: D 139 THR cc_start: 0.8935 (p) cc_final: 0.8675 (t) REVERT: D 275 ASP cc_start: 0.7251 (p0) cc_final: 0.6806 (p0) REVERT: D 477 LYS cc_start: 0.7735 (pttt) cc_final: 0.7340 (tptp) REVERT: E 267 MET cc_start: 0.8035 (tmm) cc_final: 0.7811 (ttp) REVERT: E 291 ARG cc_start: 0.8510 (mpp80) cc_final: 0.7624 (tpm170) REVERT: G 17 MET cc_start: 0.8793 (mtp) cc_final: 0.8490 (mtt) REVERT: G 51 ASP cc_start: 0.7976 (m-30) cc_final: 0.7757 (m-30) REVERT: G 102 ASN cc_start: 0.7239 (m-40) cc_final: 0.6970 (p0) REVERT: A 239 MET cc_start: 0.5237 (ptt) cc_final: 0.4885 (ptt) REVERT: A 364 PHE cc_start: 0.7822 (m-80) cc_final: 0.7503 (m-80) outliers start: 1 outliers final: 1 residues processed: 181 average time/residue: 0.1767 time to fit residues: 53.1505 Evaluate side-chains 130 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 7 optimal weight: 6.9990 chunk 324 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 318 optimal weight: 8.9990 chunk 246 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 327 optimal weight: 10.0000 chunk 342 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 216 optimal weight: 0.0020 chunk 267 optimal weight: 9.9990 overall best weight: 3.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN B 402 GLN B 431 GLN ** B1012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 ASN D 102 ASN ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 211 GLN ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.076229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.057817 restraints weight = 192985.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.058952 restraints weight = 132302.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.058811 restraints weight = 100559.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.059322 restraints weight = 81449.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.059365 restraints weight = 71301.890| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28819 Z= 0.236 Angle : 0.772 14.437 38944 Z= 0.404 Chirality : 0.047 0.254 4307 Planarity : 0.005 0.068 5056 Dihedral : 6.111 32.778 3789 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 0.07 % Allowed : 0.39 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.14), residues: 3464 helix: 0.05 (0.13), residues: 1510 sheet: -1.47 (0.29), residues: 338 loop : -2.57 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 14 TYR 0.032 0.002 TYR C 553 PHE 0.029 0.002 PHE E 251 TRP 0.025 0.002 TRP B 306 HIS 0.011 0.002 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00497 (28819) covalent geometry : angle 0.77194 (38944) hydrogen bonds : bond 0.04110 ( 1092) hydrogen bonds : angle 4.95379 ( 3189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8598 (m-80) cc_final: 0.8348 (m-10) REVERT: B 60 MET cc_start: 0.8924 (mpp) cc_final: 0.8601 (mpp) REVERT: B 130 MET cc_start: 0.8456 (mmm) cc_final: 0.7421 (mmm) REVERT: B 604 MET cc_start: 0.0005 (ttt) cc_final: -0.0624 (ttt) REVERT: B 686 PHE cc_start: 0.9207 (m-10) cc_final: 0.8908 (m-80) REVERT: B 753 MET cc_start: 0.8500 (mmm) cc_final: 0.8099 (mmm) REVERT: C 347 MET cc_start: 0.9530 (tmm) cc_final: 0.9116 (tmm) REVERT: C 348 LYS cc_start: 0.9294 (mmpt) cc_final: 0.8909 (mmmt) REVERT: C 390 MET cc_start: 0.7718 (tpt) cc_final: 0.7006 (tpp) REVERT: C 722 LYS cc_start: 0.8329 (mttt) cc_final: 0.7975 (mmtm) REVERT: C 910 MET cc_start: 0.7243 (mmp) cc_final: 0.6723 (mmm) REVERT: C 1029 GLU cc_start: 0.9084 (tp30) cc_final: 0.8748 (tp30) REVERT: D 139 THR cc_start: 0.8974 (p) cc_final: 0.8687 (t) REVERT: D 468 LEU cc_start: 0.6853 (tp) cc_final: 0.6646 (tp) REVERT: D 477 LYS cc_start: 0.8024 (pttt) cc_final: 0.7605 (tptt) REVERT: E 291 ARG cc_start: 0.8733 (mpp80) cc_final: 0.7712 (tpm170) REVERT: F 17 MET cc_start: 0.7530 (ttm) cc_final: 0.7219 (ttm) REVERT: G 17 MET cc_start: 0.8910 (mtp) cc_final: 0.8600 (mtt) REVERT: G 51 ASP cc_start: 0.8272 (m-30) cc_final: 0.8045 (m-30) REVERT: A 239 MET cc_start: 0.5915 (ptt) cc_final: 0.5130 (ptt) REVERT: A 373 GLU cc_start: 0.8762 (tt0) cc_final: 0.8536 (tp30) outliers start: 2 outliers final: 1 residues processed: 169 average time/residue: 0.1801 time to fit residues: 50.2713 Evaluate side-chains 126 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 61 optimal weight: 9.9990 chunk 205 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 339 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 GLN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 379 ASN G 43 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 GLN ** 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 = 0.3810 r_free = 0.3810 target = 0.077676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.059153 restraints weight = 191218.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.060312 restraints weight = 129335.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.060334 restraints weight = 93505.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.060697 restraints weight = 79431.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.060948 restraints weight = 68875.061| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28819 Z= 0.137 Angle : 0.663 14.420 38944 Z= 0.342 Chirality : 0.044 0.216 4307 Planarity : 0.004 0.062 5056 Dihedral : 5.792 33.157 3789 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.03 % Allowed : 0.59 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 3464 helix: 0.33 (0.14), residues: 1493 sheet: -1.32 (0.30), residues: 344 loop : -2.41 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 14 TYR 0.029 0.002 TYR C 553 PHE 0.019 0.001 PHE D 277 TRP 0.018 0.002 TRP B 306 HIS 0.008 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00294 (28819) covalent geometry : angle 0.66318 (38944) hydrogen bonds : bond 0.03612 ( 1092) hydrogen bonds : angle 4.67822 ( 3189) =============================================================================== Job complete usr+sys time: 4698.06 seconds wall clock time: 82 minutes 33.28 seconds (4953.28 seconds total)