Starting phenix.real_space_refine on Mon Jul 6 06:43:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y45_72471/07_2026/9y45_72471.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y45_72471/07_2026/9y45_72471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y45_72471/07_2026/9y45_72471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y45_72471/07_2026/9y45_72471.map" model { file = "/net/cci-nas-00/data/ceres_data/9y45_72471/07_2026/9y45_72471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y45_72471/07_2026/9y45_72471.cif" } resolution = 2.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 8 5.21 5 S 156 5.16 5 Na 4 4.78 5 C 20612 2.51 5 N 5760 2.21 5 O 6072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32612 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 8147 Classifications: {'peptide': 1014} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 57, 'TRANS': 950} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 2 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D Time building chain proxies: 10.60, per 1000 atoms: 0.33 Number of scatterers: 32612 At special positions: 0 Unit cell: (149.403, 100.476, 191.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 156 16.00 Mg 8 11.99 Na 4 11.00 O 6072 8.00 N 5760 7.00 C 20612 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: 2.73 Conformation dependent library (CDL) restraints added in 1.4 seconds 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7544 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 52 sheets defined 18.0% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 Processing helix chain 'A' and resid 13 through 14 No H-bonds generated for 'chain 'A' and resid 13 through 14' Processing helix chain 'A' and resid 15 through 19 Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.668A pdb=" N VAL A 70 " --> pdb=" O PRO A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 131 through 137 removed outlier: 3.716A pdb=" N LEU A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 199 Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 396 through 407 removed outlier: 4.102A pdb=" N TYR A 400 " --> pdb=" O HIS A 396 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 401 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 449 removed outlier: 3.964A pdb=" N MET A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 Processing helix chain 'A' and resid 520 through 526 removed outlier: 3.802A pdb=" N SER A 526 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 599 through 604 removed outlier: 4.111A pdb=" N CYS A 603 " --> pdb=" O ARG A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 625 removed outlier: 4.350A pdb=" N THR A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 620 " --> pdb=" O PRO A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 806 through 815 Processing helix chain 'A' and resid 924 through 927 Processing helix chain 'A' and resid 964 through 971 Processing helix chain 'A' and resid 973 through 977 removed outlier: 3.509A pdb=" N LEU A 977 " --> pdb=" O ARG A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1009 Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 13 through 14 No H-bonds generated for 'chain 'B' and resid 13 through 14' Processing helix chain 'B' and resid 15 through 19 Processing helix chain 'B' and resid 39 through 46 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.667A pdb=" N VAL B 70 " --> pdb=" O PRO B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 131 through 137 removed outlier: 3.716A pdb=" N LEU B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU B 137 " --> pdb=" O SER B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 199 Processing helix chain 'B' and resid 369 through 382 Processing helix chain 'B' and resid 396 through 407 removed outlier: 4.102A pdb=" N TYR B 400 " --> pdb=" O HIS B 396 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B 401 " --> pdb=" O PRO B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 449 removed outlier: 3.965A pdb=" N MET B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 480 Processing helix chain 'B' and resid 520 through 526 removed outlier: 3.801A pdb=" N SER B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 removed outlier: 3.501A pdb=" N TYR B 553 " --> pdb=" O GLY B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 604 removed outlier: 4.111A pdb=" N CYS B 603 " --> pdb=" O ARG B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 625 removed outlier: 4.350A pdb=" N THR B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU B 620 " --> pdb=" O PRO B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 795 Processing helix chain 'B' and resid 806 through 815 Processing helix chain 'B' and resid 924 through 927 Processing helix chain 'B' and resid 964 through 971 Processing helix chain 'B' and resid 973 through 977 removed outlier: 3.509A pdb=" N LEU B 977 " --> pdb=" O ARG B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1009 Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 13 through 14 No H-bonds generated for 'chain 'C' and resid 13 through 14' Processing helix chain 'C' and resid 15 through 19 Processing helix chain 'C' and resid 39 through 46 Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.667A pdb=" N VAL C 70 " --> pdb=" O PRO C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 131 through 137 removed outlier: 3.716A pdb=" N LEU C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 369 through 382 Processing helix chain 'C' and resid 396 through 407 removed outlier: 4.102A pdb=" N TYR C 400 " --> pdb=" O HIS C 396 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C 401 " --> pdb=" O PRO C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 449 removed outlier: 3.964A pdb=" N MET C 444 " --> pdb=" O ARG C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 480 Processing helix chain 'C' and resid 520 through 526 removed outlier: 3.801A pdb=" N SER C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 599 through 604 removed outlier: 4.112A pdb=" N CYS C 603 " --> pdb=" O ARG C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 625 removed outlier: 4.350A pdb=" N THR C 619 " --> pdb=" O HIS C 615 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU C 620 " --> pdb=" O PRO C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 795 Processing helix chain 'C' and resid 806 through 815 Processing helix chain 'C' and resid 924 through 927 Processing helix chain 'C' and resid 964 through 971 Processing helix chain 'C' and resid 973 through 977 removed outlier: 3.509A pdb=" N LEU C 977 " --> pdb=" O ARG C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1009 Processing helix chain 'D' and resid 7 through 12 Processing helix chain 'D' and resid 13 through 14 No H-bonds generated for 'chain 'D' and resid 13 through 14' Processing helix chain 'D' and resid 15 through 19 Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 66 through 70 removed outlier: 3.667A pdb=" N VAL D 70 " --> pdb=" O PRO D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 131 through 137 removed outlier: 3.716A pdb=" N LEU D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU D 137 " --> pdb=" O SER D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 199 Processing helix chain 'D' and resid 369 through 382 Processing helix chain 'D' and resid 396 through 407 removed outlier: 4.102A pdb=" N TYR D 400 " --> pdb=" O HIS D 396 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR D 401 " --> pdb=" O PRO D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 449 removed outlier: 3.964A pdb=" N MET D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 480 Processing helix chain 'D' and resid 520 through 526 removed outlier: 3.801A pdb=" N SER D 526 " --> pdb=" O LYS D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 599 through 604 removed outlier: 4.111A pdb=" N CYS D 603 " --> pdb=" O ARG D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 625 removed outlier: 4.350A pdb=" N THR D 619 " --> pdb=" O HIS D 615 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU D 620 " --> pdb=" O PRO D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 795 Processing helix chain 'D' and resid 806 through 815 Processing helix chain 'D' and resid 924 through 927 Processing helix chain 'D' and resid 964 through 971 Processing helix chain 'D' and resid 973 through 977 removed outlier: 3.508A pdb=" N LEU D 977 " --> pdb=" O ARG D 974 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1009 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 87 removed outlier: 8.594A pdb=" N GLU A 58 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR A 127 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 181 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 153 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102 removed outlier: 4.032A pdb=" N THR A 102 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET A 203 " --> pdb=" O THR A 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 232 removed outlier: 5.559A pdb=" N ILE A 223 " --> pdb=" O CYS A 248 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N CYS A 248 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 225 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 274 removed outlier: 6.667A pdb=" N LEU A 261 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER A 270 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A 259 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR A 272 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 257 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N LEU A 255 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR A 318 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 323 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 339 Processing sheet with id=AA7, first strand: chain 'A' and resid 485 through 486 removed outlier: 8.232A pdb=" N GLN A 486 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP A 457 " --> pdb=" O GLN A 486 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 410 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N SER A 458 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP A 412 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU A 413 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG A 353 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG A 389 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 355 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU A 534 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N PHE A 567 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 536 " --> pdb=" O PHE A 567 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 576 through 579 Processing sheet with id=AA9, first strand: chain 'A' and resid 628 through 633 Processing sheet with id=AB1, first strand: chain 'A' and resid 663 through 670 removed outlier: 6.630A pdb=" N VAL A 657 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER A 666 " --> pdb=" O TRP A 655 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP A 655 " --> pdb=" O SER A 666 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU A 668 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 653 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY A 693 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLU A 725 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU A 695 " --> pdb=" O LEU A 723 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 717 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLN A 703 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE A 715 " --> pdb=" O GLN A 703 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 740 through 743 removed outlier: 3.578A pdb=" N GLN A 768 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN A 760 " --> pdb=" O LEU A 766 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU A 766 " --> pdb=" O ASN A 760 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 777 through 784 removed outlier: 6.429A pdb=" N GLN A 888 " --> pdb=" O LEU A 778 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN A 886 " --> pdb=" O PRO A 780 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ARG A 782 " --> pdb=" O GLY A 884 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY A 884 " --> pdb=" O ARG A 782 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN A 784 " --> pdb=" O ARG A 882 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ARG A 882 " --> pdb=" O GLN A 784 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 883 " --> pdb=" O GLY A 989 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE A 990 " --> pdb=" O ASP A 955 " (cutoff:3.500A) removed outlier: 11.963A pdb=" N ASP A 955 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP A 955 " --> pdb=" O GLN A1018 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLN A1018 " --> pdb=" O ASP A 955 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N GLN A 957 " --> pdb=" O HIS A1016 " (cutoff:3.500A) removed outlier: 13.355A pdb=" N HIS A1016 " --> pdb=" O GLN A 957 " (cutoff:3.500A) removed outlier: 20.599A pdb=" N ASN A 959 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 23.639A pdb=" N ARG A1014 " --> pdb=" O ASN A 959 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP A 843 " --> pdb=" O LEU A 850 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 852 " --> pdb=" O HIS A 841 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N HIS A 841 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG A 854 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR A 839 " --> pdb=" O ARG A 854 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR A 856 " --> pdb=" O ILE A 837 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE A 837 " --> pdb=" O THR A 856 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG A 858 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 835 " --> pdb=" O ARG A 858 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA A 842 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU A 823 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN A 844 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ALA A 821 " --> pdb=" O GLN A 844 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 777 through 784 removed outlier: 6.429A pdb=" N GLN A 888 " --> pdb=" O LEU A 778 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN A 886 " --> pdb=" O PRO A 780 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ARG A 782 " --> pdb=" O GLY A 884 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY A 884 " --> pdb=" O ARG A 782 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN A 784 " --> pdb=" O ARG A 882 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ARG A 882 " --> pdb=" O GLN A 784 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 883 " --> pdb=" O GLY A 989 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE A 990 " --> pdb=" O ASP A 955 " (cutoff:3.500A) removed outlier: 11.963A pdb=" N ASP A 955 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 943 " --> pdb=" O GLY A 954 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N PHE A 956 " --> pdb=" O GLY A 941 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY A 941 " --> pdb=" O PHE A 956 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR A 942 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU A 901 " --> pdb=" O THR A 942 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 83 through 87 removed outlier: 8.593A pdb=" N GLU B 58 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR B 127 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 181 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 153 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 100 through 102 removed outlier: 4.033A pdb=" N THR B 102 " --> pdb=" O MET B 203 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET B 203 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 222 through 232 removed outlier: 5.559A pdb=" N ILE B 223 " --> pdb=" O CYS B 248 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N CYS B 248 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 225 " --> pdb=" O GLN B 246 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 266 through 274 removed outlier: 6.667A pdb=" N LEU B 261 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER B 270 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 259 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR B 272 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL B 257 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N LEU B 255 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR B 318 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU B 323 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 336 through 339 Processing sheet with id=AC2, first strand: chain 'B' and resid 485 through 486 removed outlier: 8.232A pdb=" N GLN B 486 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP B 457 " --> pdb=" O GLN B 486 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 410 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N SER B 458 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP B 412 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU B 413 " --> pdb=" O CYS B 390 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG B 353 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG B 389 " --> pdb=" O ARG B 353 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 355 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU B 534 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N PHE B 567 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B 536 " --> pdb=" O PHE B 567 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 576 through 579 Processing sheet with id=AC4, first strand: chain 'B' and resid 628 through 633 Processing sheet with id=AC5, first strand: chain 'B' and resid 663 through 670 removed outlier: 6.630A pdb=" N VAL B 657 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER B 666 " --> pdb=" O TRP B 655 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP B 655 " --> pdb=" O SER B 666 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU B 668 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU B 653 " --> pdb=" O GLU B 668 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY B 693 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLU B 725 " --> pdb=" O GLY B 693 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU B 695 " --> pdb=" O LEU B 723 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 717 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLN B 703 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE B 715 " --> pdb=" O GLN B 703 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 740 through 743 removed outlier: 3.579A pdb=" N GLN B 768 " --> pdb=" O GLN B 758 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASN B 760 " --> pdb=" O LEU B 766 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU B 766 " --> pdb=" O ASN B 760 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 777 through 784 removed outlier: 6.430A pdb=" N GLN B 888 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN B 886 " --> pdb=" O PRO B 780 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG B 782 " --> pdb=" O GLY B 884 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY B 884 " --> pdb=" O ARG B 782 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN B 784 " --> pdb=" O ARG B 882 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ARG B 882 " --> pdb=" O GLN B 784 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE B 883 " --> pdb=" O GLY B 989 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE B 990 " --> pdb=" O ASP B 955 " (cutoff:3.500A) removed outlier: 11.962A pdb=" N ASP B 955 " --> pdb=" O PHE B 990 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP B 955 " --> pdb=" O GLN B1018 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLN B1018 " --> pdb=" O ASP B 955 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N GLN B 957 " --> pdb=" O HIS B1016 " (cutoff:3.500A) removed outlier: 13.355A pdb=" N HIS B1016 " --> pdb=" O GLN B 957 " (cutoff:3.500A) removed outlier: 20.599A pdb=" N ASN B 959 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 23.639A pdb=" N ARG B1014 " --> pdb=" O ASN B 959 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP B 843 " --> pdb=" O LEU B 850 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE B 852 " --> pdb=" O HIS B 841 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N HIS B 841 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG B 854 " --> pdb=" O THR B 839 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR B 839 " --> pdb=" O ARG B 854 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR B 856 " --> pdb=" O ILE B 837 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE B 837 " --> pdb=" O THR B 856 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG B 858 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B 835 " --> pdb=" O ARG B 858 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA B 842 " --> pdb=" O LEU B 823 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU B 823 " --> pdb=" O ALA B 842 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN B 844 " --> pdb=" O ALA B 821 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ALA B 821 " --> pdb=" O GLN B 844 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 777 through 784 removed outlier: 6.430A pdb=" N GLN B 888 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN B 886 " --> pdb=" O PRO B 780 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG B 782 " --> pdb=" O GLY B 884 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY B 884 " --> pdb=" O ARG B 782 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN B 784 " --> pdb=" O ARG B 882 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ARG B 882 " --> pdb=" O GLN B 784 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE B 883 " --> pdb=" O GLY B 989 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE B 990 " --> pdb=" O ASP B 955 " (cutoff:3.500A) removed outlier: 11.962A pdb=" N ASP B 955 " --> pdb=" O PHE B 990 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG B 943 " --> pdb=" O GLY B 954 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE B 956 " --> pdb=" O GLY B 941 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY B 941 " --> pdb=" O PHE B 956 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR B 942 " --> pdb=" O LEU B 901 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU B 901 " --> pdb=" O THR B 942 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AD1, first strand: chain 'C' and resid 83 through 87 removed outlier: 8.592A pdb=" N GLU C 58 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR C 127 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY C 181 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU C 153 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 100 through 102 removed outlier: 4.032A pdb=" N THR C 102 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET C 203 " --> pdb=" O THR C 102 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 222 through 232 removed outlier: 5.558A pdb=" N ILE C 223 " --> pdb=" O CYS C 248 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N CYS C 248 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP C 225 " --> pdb=" O GLN C 246 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 266 through 274 removed outlier: 6.667A pdb=" N LEU C 261 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER C 270 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL C 259 " --> pdb=" O SER C 270 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR C 272 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL C 257 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N LEU C 255 " --> pdb=" O PRO C 274 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR C 318 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU C 323 " --> pdb=" O THR C 318 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 336 through 339 Processing sheet with id=AD6, first strand: chain 'C' and resid 485 through 486 removed outlier: 8.232A pdb=" N GLN C 486 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP C 457 " --> pdb=" O GLN C 486 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 410 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N SER C 458 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP C 412 " --> pdb=" O SER C 458 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU C 413 " --> pdb=" O CYS C 390 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG C 353 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG C 389 " --> pdb=" O ARG C 353 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C 355 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU C 534 " --> pdb=" O GLY C 565 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N PHE C 567 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU C 536 " --> pdb=" O PHE C 567 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 576 through 579 Processing sheet with id=AD8, first strand: chain 'C' and resid 628 through 633 Processing sheet with id=AD9, first strand: chain 'C' and resid 663 through 670 removed outlier: 6.631A pdb=" N VAL C 657 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER C 666 " --> pdb=" O TRP C 655 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP C 655 " --> pdb=" O SER C 666 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU C 668 " --> pdb=" O LEU C 653 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU C 653 " --> pdb=" O GLU C 668 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY C 693 " --> pdb=" O GLU C 725 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLU C 725 " --> pdb=" O GLY C 693 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU C 695 " --> pdb=" O LEU C 723 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA C 717 " --> pdb=" O VAL C 701 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN C 703 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE C 715 " --> pdb=" O GLN C 703 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 740 through 743 removed outlier: 3.578A pdb=" N GLN C 768 " --> pdb=" O GLN C 758 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASN C 760 " --> pdb=" O LEU C 766 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU C 766 " --> pdb=" O ASN C 760 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 777 through 784 removed outlier: 6.429A pdb=" N GLN C 888 " --> pdb=" O LEU C 778 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN C 886 " --> pdb=" O PRO C 780 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG C 782 " --> pdb=" O GLY C 884 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY C 884 " --> pdb=" O ARG C 782 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN C 784 " --> pdb=" O ARG C 882 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ARG C 882 " --> pdb=" O GLN C 784 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE C 883 " --> pdb=" O GLY C 989 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE C 990 " --> pdb=" O ASP C 955 " (cutoff:3.500A) removed outlier: 11.962A pdb=" N ASP C 955 " --> pdb=" O PHE C 990 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP C 955 " --> pdb=" O GLN C1018 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN C1018 " --> pdb=" O ASP C 955 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N GLN C 957 " --> pdb=" O HIS C1016 " (cutoff:3.500A) removed outlier: 13.355A pdb=" N HIS C1016 " --> pdb=" O GLN C 957 " (cutoff:3.500A) removed outlier: 20.598A pdb=" N ASN C 959 " --> pdb=" O ARG C1014 " (cutoff:3.500A) removed outlier: 23.639A pdb=" N ARG C1014 " --> pdb=" O ASN C 959 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP C 843 " --> pdb=" O LEU C 850 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE C 852 " --> pdb=" O HIS C 841 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N HIS C 841 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG C 854 " --> pdb=" O THR C 839 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR C 839 " --> pdb=" O ARG C 854 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR C 856 " --> pdb=" O ILE C 837 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE C 837 " --> pdb=" O THR C 856 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG C 858 " --> pdb=" O VAL C 835 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL C 835 " --> pdb=" O ARG C 858 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA C 842 " --> pdb=" O LEU C 823 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU C 823 " --> pdb=" O ALA C 842 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN C 844 " --> pdb=" O ALA C 821 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ALA C 821 " --> pdb=" O GLN C 844 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 777 through 784 removed outlier: 6.429A pdb=" N GLN C 888 " --> pdb=" O LEU C 778 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN C 886 " --> pdb=" O PRO C 780 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG C 782 " --> pdb=" O GLY C 884 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY C 884 " --> pdb=" O ARG C 782 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN C 784 " --> pdb=" O ARG C 882 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ARG C 882 " --> pdb=" O GLN C 784 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE C 883 " --> pdb=" O GLY C 989 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE C 990 " --> pdb=" O ASP C 955 " (cutoff:3.500A) removed outlier: 11.962A pdb=" N ASP C 955 " --> pdb=" O PHE C 990 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG C 943 " --> pdb=" O GLY C 954 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N PHE C 956 " --> pdb=" O GLY C 941 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY C 941 " --> pdb=" O PHE C 956 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR C 942 " --> pdb=" O LEU C 901 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU C 901 " --> pdb=" O THR C 942 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 52 through 54 Processing sheet with id=AE5, first strand: chain 'D' and resid 83 through 87 removed outlier: 8.593A pdb=" N GLU D 58 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR D 127 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY D 181 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU D 153 " --> pdb=" O VAL D 160 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 100 through 102 removed outlier: 4.032A pdb=" N THR D 102 " --> pdb=" O MET D 203 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET D 203 " --> pdb=" O THR D 102 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 222 through 232 removed outlier: 5.558A pdb=" N ILE D 223 " --> pdb=" O CYS D 248 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N CYS D 248 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP D 225 " --> pdb=" O GLN D 246 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 266 through 274 removed outlier: 6.667A pdb=" N LEU D 261 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER D 270 " --> pdb=" O VAL D 259 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL D 259 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR D 272 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL D 257 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N LEU D 255 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR D 318 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU D 323 " --> pdb=" O THR D 318 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 336 through 339 Processing sheet with id=AF1, first strand: chain 'D' and resid 485 through 486 removed outlier: 8.232A pdb=" N GLN D 486 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP D 457 " --> pdb=" O GLN D 486 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL D 410 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N SER D 458 " --> pdb=" O VAL D 410 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP D 412 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU D 413 " --> pdb=" O CYS D 390 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG D 353 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG D 389 " --> pdb=" O ARG D 353 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL D 355 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU D 534 " --> pdb=" O GLY D 565 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N PHE D 567 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 536 " --> pdb=" O PHE D 567 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 576 through 579 Processing sheet with id=AF3, first strand: chain 'D' and resid 628 through 633 Processing sheet with id=AF4, first strand: chain 'D' and resid 663 through 670 removed outlier: 6.630A pdb=" N VAL D 657 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER D 666 " --> pdb=" O TRP D 655 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP D 655 " --> pdb=" O SER D 666 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU D 668 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU D 653 " --> pdb=" O GLU D 668 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY D 693 " --> pdb=" O GLU D 725 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLU D 725 " --> pdb=" O GLY D 693 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU D 695 " --> pdb=" O LEU D 723 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA D 717 " --> pdb=" O VAL D 701 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLN D 703 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE D 715 " --> pdb=" O GLN D 703 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 740 through 743 removed outlier: 3.578A pdb=" N GLN D 768 " --> pdb=" O GLN D 758 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASN D 760 " --> pdb=" O LEU D 766 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU D 766 " --> pdb=" O ASN D 760 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 777 through 784 removed outlier: 6.429A pdb=" N GLN D 888 " --> pdb=" O LEU D 778 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN D 886 " --> pdb=" O PRO D 780 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG D 782 " --> pdb=" O GLY D 884 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY D 884 " --> pdb=" O ARG D 782 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN D 784 " --> pdb=" O ARG D 882 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ARG D 882 " --> pdb=" O GLN D 784 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE D 883 " --> pdb=" O GLY D 989 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE D 990 " --> pdb=" O ASP D 955 " (cutoff:3.500A) removed outlier: 11.962A pdb=" N ASP D 955 " --> pdb=" O PHE D 990 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP D 955 " --> pdb=" O GLN D1018 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLN D1018 " --> pdb=" O ASP D 955 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N GLN D 957 " --> pdb=" O HIS D1016 " (cutoff:3.500A) removed outlier: 13.355A pdb=" N HIS D1016 " --> pdb=" O GLN D 957 " (cutoff:3.500A) removed outlier: 20.599A pdb=" N ASN D 959 " --> pdb=" O ARG D1014 " (cutoff:3.500A) removed outlier: 23.640A pdb=" N ARG D1014 " --> pdb=" O ASN D 959 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP D 843 " --> pdb=" O LEU D 850 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE D 852 " --> pdb=" O HIS D 841 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N HIS D 841 " --> pdb=" O ILE D 852 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG D 854 " --> pdb=" O THR D 839 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR D 839 " --> pdb=" O ARG D 854 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR D 856 " --> pdb=" O ILE D 837 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE D 837 " --> pdb=" O THR D 856 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG D 858 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL D 835 " --> pdb=" O ARG D 858 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA D 842 " --> pdb=" O LEU D 823 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU D 823 " --> pdb=" O ALA D 842 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN D 844 " --> pdb=" O ALA D 821 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ALA D 821 " --> pdb=" O GLN D 844 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 777 through 784 removed outlier: 6.429A pdb=" N GLN D 888 " --> pdb=" O LEU D 778 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN D 886 " --> pdb=" O PRO D 780 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG D 782 " --> pdb=" O GLY D 884 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY D 884 " --> pdb=" O ARG D 782 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN D 784 " --> pdb=" O ARG D 882 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ARG D 882 " --> pdb=" O GLN D 784 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE D 883 " --> pdb=" O GLY D 989 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE D 990 " --> pdb=" O ASP D 955 " (cutoff:3.500A) removed outlier: 11.962A pdb=" N ASP D 955 " --> pdb=" O PHE D 990 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG D 943 " --> pdb=" O GLY D 954 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N PHE D 956 " --> pdb=" O GLY D 941 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY D 941 " --> pdb=" O PHE D 956 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR D 942 " --> pdb=" O LEU D 901 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU D 901 " --> pdb=" O THR D 942 " (cutoff:3.500A) 1195 hydrogen bonds defined for protein. 3081 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: 8.94 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8218 1.33 - 1.45: 7224 1.45 - 1.57: 17854 1.57 - 1.69: 0 1.69 - 1.81: 248 Bond restraints: 33544 Sorted by residual: bond pdb=" N MET A 424 " pdb=" CA MET A 424 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.27e-02 6.20e+03 9.10e+00 bond pdb=" N MET B 424 " pdb=" CA MET B 424 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.27e-02 6.20e+03 9.10e+00 bond pdb=" N MET C 424 " pdb=" CA MET C 424 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.27e-02 6.20e+03 9.10e+00 bond pdb=" N MET D 424 " pdb=" CA MET D 424 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.27e-02 6.20e+03 9.02e+00 bond pdb=" N VAL B 422 " pdb=" CA VAL B 422 " ideal model delta sigma weight residual 1.461 1.496 -0.034 1.23e-02 6.61e+03 7.79e+00 ... (remaining 33539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 44044 1.59 - 3.18: 1384 3.18 - 4.77: 292 4.77 - 6.35: 24 6.35 - 7.94: 16 Bond angle restraints: 45760 Sorted by residual: angle pdb=" CA HIS A 419 " pdb=" C HIS A 419 " pdb=" O HIS A 419 " ideal model delta sigma weight residual 120.63 116.15 4.48 1.08e+00 8.57e-01 1.72e+01 angle pdb=" CA HIS C 419 " pdb=" C HIS C 419 " pdb=" O HIS C 419 " ideal model delta sigma weight residual 120.63 116.15 4.48 1.08e+00 8.57e-01 1.72e+01 angle pdb=" CA HIS D 419 " pdb=" C HIS D 419 " pdb=" O HIS D 419 " ideal model delta sigma weight residual 120.63 116.16 4.47 1.08e+00 8.57e-01 1.71e+01 angle pdb=" CA HIS B 419 " pdb=" C HIS B 419 " pdb=" O HIS B 419 " ideal model delta sigma weight residual 120.63 116.19 4.44 1.08e+00 8.57e-01 1.69e+01 angle pdb=" CA TRP C 554 " pdb=" CB TRP C 554 " pdb=" CG TRP C 554 " ideal model delta sigma weight residual 113.60 106.27 7.33 1.90e+00 2.77e-01 1.49e+01 ... (remaining 45755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 17117 17.77 - 35.54: 1763 35.54 - 53.31: 548 53.31 - 71.09: 132 71.09 - 88.86: 80 Dihedral angle restraints: 19640 sinusoidal: 7924 harmonic: 11716 Sorted by residual: dihedral pdb=" CA THR A 596 " pdb=" C THR A 596 " pdb=" N PRO A 597 " pdb=" CA PRO A 597 " ideal model delta harmonic sigma weight residual 180.00 -155.15 -24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA THR C 596 " pdb=" C THR C 596 " pdb=" N PRO C 597 " pdb=" CA PRO C 597 " ideal model delta harmonic sigma weight residual -180.00 -155.15 -24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA THR D 596 " pdb=" C THR D 596 " pdb=" N PRO D 597 " pdb=" CA PRO D 597 " ideal model delta harmonic sigma weight residual -180.00 -155.15 -24.85 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 19637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2613 0.032 - 0.064: 1392 0.064 - 0.096: 477 0.096 - 0.128: 264 0.128 - 0.161: 38 Chirality restraints: 4784 Sorted by residual: chirality pdb=" CA HIS B 419 " pdb=" N HIS B 419 " pdb=" C HIS B 419 " pdb=" CB HIS B 419 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CA HIS D 419 " pdb=" N HIS D 419 " pdb=" C HIS D 419 " pdb=" CB HIS D 419 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA HIS C 419 " pdb=" N HIS C 419 " pdb=" C HIS C 419 " pdb=" CB HIS C 419 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.18e-01 ... (remaining 4781 not shown) Planarity restraints: 6040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 421 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C MET B 421 " -0.037 2.00e-02 2.50e+03 pdb=" O MET B 421 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 422 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 421 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C MET D 421 " 0.037 2.00e-02 2.50e+03 pdb=" O MET D 421 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL D 422 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 421 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" C MET A 421 " -0.037 2.00e-02 2.50e+03 pdb=" O MET A 421 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A 422 " 0.013 2.00e-02 2.50e+03 ... (remaining 6037 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 52 2.36 - 2.99: 16187 2.99 - 3.63: 49941 3.63 - 4.26: 87462 4.26 - 4.90: 140669 Nonbonded interactions: 294311 Sorted by model distance: nonbonded pdb=" OE2 GLU C 417 " pdb="MG MG C2001 " model vdw 1.724 2.170 nonbonded pdb=" OE2 GLU A 417 " pdb="MG MG A2001 " model vdw 1.725 2.170 nonbonded pdb=" OE2 GLU D 417 " pdb="MG MG D2001 " model vdw 1.725 2.170 nonbonded pdb=" OE2 GLU B 417 " pdb="MG MG B2001 " model vdw 1.725 2.170 nonbonded pdb=" O VAL C 22 " pdb="MG MG C2002 " model vdw 1.739 2.170 ... (remaining 294306 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 35.980 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 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 0.041 33544 Z= 0.225 Angle : 0.692 7.942 45760 Z= 0.389 Chirality : 0.048 0.161 4784 Planarity : 0.005 0.034 6040 Dihedral : 17.413 88.856 12096 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.07 % Favored : 96.73 % Rotamer: Outliers : 0.69 % Allowed : 19.12 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.13), residues: 4040 helix: -0.15 (0.22), residues: 532 sheet: 0.69 (0.13), residues: 1400 loop : -0.04 (0.14), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 858 TYR 0.030 0.002 TYR D 101 PHE 0.012 0.002 PHE A 990 TRP 0.032 0.002 TRP B 554 HIS 0.005 0.001 HIS D 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.22 (33544) covalent geometry : angle 0.69218 / 0.39 (45760) hydrogen bonds : bond 0.18178 / 12.11 ( 1139) hydrogen bonds : angle 7.28498 / 5.15 ( 3081) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 492 time to evaluate : 1.256 Fit side-chains REVERT: A 188 MET cc_start: 0.9071 (ttm) cc_final: 0.8823 (ttp) REVERT: A 439 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: B 188 MET cc_start: 0.9074 (ttm) cc_final: 0.8840 (ttp) REVERT: B 439 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: C 188 MET cc_start: 0.9075 (ttm) cc_final: 0.8841 (ttp) REVERT: C 439 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: D 188 MET cc_start: 0.9070 (ttm) cc_final: 0.8827 (ttp) REVERT: D 439 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7613 (mp0) outliers start: 24 outliers final: 14 residues processed: 503 average time/residue: 0.8729 time to fit residues: 505.8018 Evaluate side-chains 496 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 478 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 856 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN A 136 GLN A 246 GLN A 605 ASN A 625 GLN A 635 GLN A 758 GLN A 762 GLN A 845 HIS A 897 ASN A 946 ASN A 951 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN B 39 ASN B 136 GLN B 246 GLN B 605 ASN B 625 GLN B 758 GLN B 762 GLN B 845 HIS B 897 ASN B 946 ASN B 951 GLN ** B 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN C 39 ASN C 136 GLN C 246 GLN C 625 GLN C 758 GLN C 762 GLN C 845 HIS C 897 ASN C 946 ASN C 951 GLN ** C 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 967 GLN D 39 ASN D 136 GLN D 246 GLN D 605 ASN D 625 GLN D 635 GLN D 758 GLN D 762 GLN D 845 HIS D 897 ASN D 946 ASN D 951 GLN ** D 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 967 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.142267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124378 restraints weight = 31318.182| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 0.93 r_work: 0.3272 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33544 Z= 0.175 Angle : 0.621 7.376 45760 Z= 0.331 Chirality : 0.047 0.147 4784 Planarity : 0.005 0.043 6040 Dihedral : 6.387 63.657 4467 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.72 % Favored : 97.08 % Rotamer: Outliers : 3.08 % Allowed : 16.30 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.13), residues: 4040 helix: -0.07 (0.22), residues: 536 sheet: 0.69 (0.14), residues: 1360 loop : -0.02 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1014 TYR 0.028 0.002 TYR D 101 PHE 0.013 0.002 PHE B 990 TRP 0.033 0.002 TRP B 554 HIS 0.005 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (33544) covalent geometry : angle 0.62139 / 0.33 (45760) hydrogen bonds : bond 0.05393 / 3.57 ( 1139) hydrogen bonds : angle 5.82509 / 4.12 ( 3081) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 485 time to evaluate : 1.282 Fit side-chains REVERT: A 188 MET cc_start: 0.9071 (ttm) cc_final: 0.8804 (ttp) REVERT: A 439 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: A 738 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7510 (tt) REVERT: A 1014 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7588 (mtm-85) REVERT: B 188 MET cc_start: 0.9076 (ttm) cc_final: 0.8818 (ttp) REVERT: B 439 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: B 738 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7538 (tt) REVERT: B 1014 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7588 (mtm-85) REVERT: C 188 MET cc_start: 0.9073 (ttm) cc_final: 0.8813 (ttp) REVERT: C 439 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: C 738 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7540 (tt) REVERT: C 1014 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7601 (mtm-85) REVERT: D 188 MET cc_start: 0.9072 (ttm) cc_final: 0.8808 (ttp) REVERT: D 439 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: D 738 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7515 (tt) REVERT: D 1014 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7584 (mtm-85) outliers start: 107 outliers final: 34 residues processed: 542 average time/residue: 0.7847 time to fit residues: 495.3941 Evaluate side-chains 515 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 469 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 662 LYS Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 662 LYS Chi-restraints excluded: chain C residue 738 ILE Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 662 LYS Chi-restraints excluded: chain D residue 738 ILE Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 856 THR Chi-restraints excluded: chain D residue 1014 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 38 optimal weight: 5.9990 chunk 297 optimal weight: 0.9990 chunk 173 optimal weight: 9.9990 chunk 373 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 198 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN A 94 HIS A 136 GLN A 246 GLN A 762 GLN A 967 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN B 94 HIS B 136 GLN B 246 GLN B 635 GLN B 762 GLN B 967 GLN ** B 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 94 HIS C 136 GLN C 246 GLN C 605 ASN C 635 GLN C 762 GLN C 967 GLN ** C 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN D 94 HIS D 136 GLN D 246 GLN D 762 GLN D 967 GLN ** D 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.142098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124219 restraints weight = 31189.062| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 0.92 r_work: 0.3271 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33544 Z= 0.173 Angle : 0.608 7.294 45760 Z= 0.323 Chirality : 0.047 0.219 4784 Planarity : 0.005 0.036 6040 Dihedral : 6.304 63.467 4460 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.87 % Favored : 96.93 % Rotamer: Outliers : 2.88 % Allowed : 16.42 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.13), residues: 4040 helix: -0.06 (0.22), residues: 536 sheet: 0.69 (0.13), residues: 1396 loop : -0.03 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 858 TYR 0.029 0.002 TYR C 101 PHE 0.013 0.002 PHE D 990 TRP 0.033 0.002 TRP B 554 HIS 0.005 0.001 HIS C 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (33544) covalent geometry : angle 0.60813 / 0.32 (45760) hydrogen bonds : bond 0.05034 / 3.34 ( 1139) hydrogen bonds : angle 5.61907 / 3.97 ( 3081) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 479 time to evaluate : 1.315 Fit side-chains REVERT: A 3 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6101 (tmt) REVERT: A 235 ASP cc_start: 0.8378 (p0) cc_final: 0.8145 (p0) REVERT: A 244 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: A 439 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: A 738 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7483 (tt) REVERT: A 769 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7553 (tmt) REVERT: A 967 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8627 (tt0) REVERT: B 3 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6892 (tmm) REVERT: B 235 ASP cc_start: 0.8376 (p0) cc_final: 0.8171 (p0) REVERT: B 439 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: B 738 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7500 (tt) REVERT: B 798 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: C 3 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6874 (tmm) REVERT: C 439 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: C 738 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7506 (tt) REVERT: C 798 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8061 (pt0) REVERT: C 967 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8642 (tt0) REVERT: D 3 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6089 (tmt) REVERT: D 244 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: D 439 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: D 738 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7496 (tt) REVERT: D 769 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7555 (tmt) REVERT: D 967 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8648 (tt0) outliers start: 100 outliers final: 36 residues processed: 525 average time/residue: 0.7774 time to fit residues: 473.8041 Evaluate side-chains 528 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 471 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 967 GLN Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 662 LYS Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 662 LYS Chi-restraints excluded: chain C residue 738 ILE Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 967 GLN Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 738 ILE Chi-restraints excluded: chain D residue 769 MET Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 798 GLU Chi-restraints excluded: chain D residue 856 THR Chi-restraints excluded: chain D residue 967 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 316 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 0.0970 chunk 214 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 339 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 327 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 33 optimal weight: 0.0770 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN A 136 GLN A 246 GLN A 635 GLN A 762 GLN A 891 GLN A 967 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN B 136 GLN B 246 GLN B 635 GLN B 891 GLN B 967 GLN ** B 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 136 GLN C 246 GLN C 635 GLN C 762 GLN C 891 GLN C 967 GLN ** C 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN D 136 GLN D 246 GLN D 635 GLN D 891 GLN D 967 GLN ** D 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.144559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.126862 restraints weight = 31101.006| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 0.93 r_work: 0.3294 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33544 Z= 0.123 Angle : 0.547 6.668 45760 Z= 0.289 Chirality : 0.045 0.160 4784 Planarity : 0.004 0.033 6040 Dihedral : 5.995 61.849 4460 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.80 % Favored : 97.00 % Rotamer: Outliers : 2.07 % Allowed : 17.37 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.13), residues: 4040 helix: 0.24 (0.22), residues: 524 sheet: 0.73 (0.13), residues: 1396 loop : -0.06 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 858 TYR 0.023 0.002 TYR C 101 PHE 0.009 0.001 PHE D 990 TRP 0.030 0.002 TRP B 554 HIS 0.004 0.001 HIS C 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (33544) covalent geometry : angle 0.54741 / 0.29 (45760) hydrogen bonds : bond 0.04212 / 2.78 ( 1139) hydrogen bonds : angle 5.38575 / 3.82 ( 3081) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 487 time to evaluate : 1.229 Fit side-chains REVERT: A 3 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6070 (tmt) REVERT: A 244 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: A 439 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: A 798 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8046 (pt0) REVERT: B 3 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6073 (tmt) REVERT: B 244 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: B 439 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: B 798 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8062 (pt0) REVERT: C 3 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6045 (tmt) REVERT: C 244 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: C 439 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: C 798 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8045 (pt0) REVERT: D 3 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6046 (tmt) REVERT: D 244 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: D 439 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: D 798 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8061 (pt0) outliers start: 72 outliers final: 21 residues processed: 518 average time/residue: 0.7846 time to fit residues: 470.2817 Evaluate side-chains 503 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 466 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 662 LYS Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 662 LYS Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 798 GLU Chi-restraints excluded: chain D residue 856 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 186 optimal weight: 8.9990 chunk 158 optimal weight: 8.9990 chunk 220 optimal weight: 4.9990 chunk 256 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 300 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 367 optimal weight: 0.6980 chunk 246 optimal weight: 6.9990 chunk 143 optimal weight: 0.0370 chunk 45 optimal weight: 5.9990 overall best weight: 1.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN A 136 GLN A 246 GLN A 967 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN B 136 GLN B 246 GLN B 967 GLN ** B 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 136 GLN C 246 GLN C 762 GLN C 967 GLN ** C 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN D 136 GLN D 246 GLN D 967 GLN ** D 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.141656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.123779 restraints weight = 31178.345| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 0.92 r_work: 0.3264 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33544 Z= 0.198 Angle : 0.624 7.639 45760 Z= 0.330 Chirality : 0.048 0.194 4784 Planarity : 0.005 0.035 6040 Dihedral : 6.343 62.724 4460 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.07 % Favored : 96.73 % Rotamer: Outliers : 2.42 % Allowed : 16.94 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.13), residues: 4040 helix: 0.15 (0.22), residues: 512 sheet: 0.71 (0.14), residues: 1356 loop : -0.09 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 858 TYR 0.031 0.002 TYR D 101 PHE 0.014 0.002 PHE B 990 TRP 0.033 0.002 TRP B 554 HIS 0.005 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (33544) covalent geometry : angle 0.62421 / 0.33 (45760) hydrogen bonds : bond 0.05010 / 3.34 ( 1139) hydrogen bonds : angle 5.51250 / 3.89 ( 3081) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 483 time to evaluate : 1.151 Fit side-chains REVERT: A 3 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6129 (tmt) REVERT: A 244 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7874 (tm-30) REVERT: A 335 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8663 (tt0) REVERT: A 439 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: A 798 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8039 (pt0) REVERT: B 3 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6141 (tmt) REVERT: B 244 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: B 335 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8654 (tt0) REVERT: B 439 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: B 798 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8056 (pt0) REVERT: C 3 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6117 (tmt) REVERT: C 244 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: C 335 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8660 (tt0) REVERT: C 439 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: C 798 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: D 3 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6116 (tmt) REVERT: D 244 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: D 335 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8651 (tt0) REVERT: D 439 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: D 798 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8051 (pt0) REVERT: D 904 GLN cc_start: 0.8172 (mt0) cc_final: 0.7318 (pm20) outliers start: 84 outliers final: 34 residues processed: 523 average time/residue: 0.8003 time to fit residues: 484.2158 Evaluate side-chains 520 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 466 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 760 ASN Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 967 GLN Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 662 LYS Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 662 LYS Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 760 ASN Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 798 GLU Chi-restraints excluded: chain D residue 856 THR Chi-restraints excluded: chain D residue 967 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 283 optimal weight: 0.3980 chunk 383 optimal weight: 5.9990 chunk 258 optimal weight: 4.9990 chunk 362 optimal weight: 0.9990 chunk 361 optimal weight: 0.5980 chunk 262 optimal weight: 4.9990 chunk 397 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 327 optimal weight: 0.8980 chunk 289 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN A 136 GLN A 246 GLN A 635 GLN A 967 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN B 136 GLN B 246 GLN B 635 GLN ** B 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN ** B 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 136 GLN C 246 GLN C 635 GLN ** C 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 967 GLN ** C 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN D 136 GLN D 246 GLN D 635 GLN D 967 GLN ** D 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.144975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.127393 restraints weight = 31091.523| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 0.92 r_work: 0.3312 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33544 Z= 0.114 Angle : 0.539 7.382 45760 Z= 0.284 Chirality : 0.044 0.142 4784 Planarity : 0.004 0.033 6040 Dihedral : 5.945 60.955 4460 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.92 % Favored : 96.88 % Rotamer: Outliers : 1.67 % Allowed : 17.71 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.13), residues: 4040 helix: 0.28 (0.22), residues: 524 sheet: 0.78 (0.13), residues: 1388 loop : -0.09 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 858 TYR 0.021 0.002 TYR A 101 PHE 0.009 0.001 PHE A 990 TRP 0.030 0.002 TRP B 554 HIS 0.003 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (33544) covalent geometry : angle 0.53907 / 0.28 (45760) hydrogen bonds : bond 0.03978 / 2.63 ( 1139) hydrogen bonds : angle 5.26847 / 3.73 ( 3081) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 471 time to evaluate : 1.366 Fit side-chains REVERT: A 3 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6056 (tmt) REVERT: A 439 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: A 798 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8045 (pt0) REVERT: A 1014 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7608 (mtm-85) REVERT: B 3 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6112 (tmt) REVERT: B 439 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: B 798 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8066 (pt0) REVERT: B 1014 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7594 (mtm-85) REVERT: C 3 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6086 (tmt) REVERT: C 439 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: C 798 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8047 (pt0) REVERT: C 1014 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7604 (mtm-85) REVERT: D 3 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6030 (tmt) REVERT: D 439 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: D 798 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8063 (pt0) REVERT: D 1014 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7595 (mtm-85) outliers start: 58 outliers final: 23 residues processed: 495 average time/residue: 0.8057 time to fit residues: 462.8502 Evaluate side-chains 498 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 463 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 760 ASN Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 662 LYS Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 662 LYS Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 798 GLU Chi-restraints excluded: chain D residue 856 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 68 optimal weight: 8.9990 chunk 301 optimal weight: 0.7980 chunk 304 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 305 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 351 optimal weight: 1.9990 chunk 348 optimal weight: 0.0470 chunk 387 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 221 optimal weight: 3.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN A 136 GLN A 246 GLN A 635 GLN A 967 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN B 136 GLN B 246 GLN B 635 GLN B 967 GLN ** B 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 136 GLN C 246 GLN C 635 GLN C 967 GLN ** C 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN D 136 GLN D 246 GLN D 635 GLN D 967 GLN ** D 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.124671 restraints weight = 31157.528| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 0.92 r_work: 0.3275 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33544 Z= 0.170 Angle : 0.597 7.800 45760 Z= 0.315 Chirality : 0.047 0.165 4784 Planarity : 0.005 0.034 6040 Dihedral : 6.196 62.132 4460 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.87 % Favored : 96.93 % Rotamer: Outliers : 2.33 % Allowed : 17.28 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.13), residues: 4040 helix: 0.26 (0.22), residues: 512 sheet: 0.79 (0.14), residues: 1388 loop : -0.08 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 858 TYR 0.030 0.002 TYR D 101 PHE 0.012 0.002 PHE A 990 TRP 0.031 0.002 TRP B 554 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (33544) covalent geometry : angle 0.59676 / 0.31 (45760) hydrogen bonds : bond 0.04658 / 3.10 ( 1139) hydrogen bonds : angle 5.38461 / 3.80 ( 3081) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 473 time to evaluate : 1.248 Fit side-chains REVERT: A 3 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6106 (tmt) REVERT: A 439 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: A 798 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8032 (pt0) REVERT: A 1014 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7673 (mtm-85) REVERT: B 3 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6102 (tmt) REVERT: B 439 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: B 769 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7598 (tmt) REVERT: B 1014 ARG cc_start: 0.7945 (mtm-85) cc_final: 0.7677 (mtm-85) REVERT: C 3 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6077 (tmt) REVERT: C 439 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: C 1014 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7689 (mtm-85) REVERT: D 3 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6094 (tmt) REVERT: D 439 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: D 798 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8046 (pt0) REVERT: D 1014 ARG cc_start: 0.7940 (mtm-85) cc_final: 0.7677 (mtm-85) outliers start: 81 outliers final: 35 residues processed: 515 average time/residue: 0.7681 time to fit residues: 457.8995 Evaluate side-chains 510 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 464 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 760 ASN Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 967 GLN Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 662 LYS Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 769 MET Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 662 LYS Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 760 ASN Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 798 GLU Chi-restraints excluded: chain D residue 856 THR Chi-restraints excluded: chain D residue 967 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 223 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 315 optimal weight: 8.9990 chunk 335 optimal weight: 0.8980 chunk 198 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 345 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 225 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN A 136 GLN A 246 GLN A 635 GLN A 967 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN B 136 GLN B 246 GLN B 635 GLN B 967 GLN ** B 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 136 GLN C 246 GLN C 635 GLN C 967 GLN ** C 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN D 136 GLN D 246 GLN D 635 GLN D 967 GLN ** D 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124698 restraints weight = 31192.262| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 0.92 r_work: 0.3279 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33544 Z= 0.169 Angle : 0.597 8.255 45760 Z= 0.315 Chirality : 0.046 0.161 4784 Planarity : 0.005 0.034 6040 Dihedral : 6.210 61.752 4460 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.77 % Favored : 97.03 % Rotamer: Outliers : 1.99 % Allowed : 17.48 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.13), residues: 4040 helix: 0.25 (0.22), residues: 512 sheet: 0.78 (0.14), residues: 1388 loop : -0.10 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 858 TYR 0.029 0.002 TYR A 101 PHE 0.013 0.002 PHE A 990 TRP 0.031 0.002 TRP B 554 HIS 0.004 0.001 HIS D 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (33544) covalent geometry : angle 0.59738 / 0.31 (45760) hydrogen bonds : bond 0.04627 / 3.08 ( 1139) hydrogen bonds : angle 5.37671 / 3.79 ( 3081) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 463 time to evaluate : 0.866 Fit side-chains REVERT: A 3 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6125 (tmt) REVERT: A 244 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: A 439 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: A 798 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: A 1014 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7663 (mtm-85) REVERT: B 3 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6110 (tmt) REVERT: B 439 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: B 1014 ARG cc_start: 0.7937 (mtm-85) cc_final: 0.7667 (mtm-85) REVERT: C 3 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6069 (tmt) REVERT: C 439 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: C 1014 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7682 (mtm-85) REVERT: D 3 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6106 (tmt) REVERT: D 439 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: D 798 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8039 (pt0) REVERT: D 1014 ARG cc_start: 0.7934 (mtm-85) cc_final: 0.7670 (mtm-85) outliers start: 69 outliers final: 34 residues processed: 493 average time/residue: 0.8079 time to fit residues: 460.3274 Evaluate side-chains 507 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 462 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 760 ASN Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 662 LYS Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 662 LYS Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 798 GLU Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 760 ASN Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 798 GLU Chi-restraints excluded: chain D residue 856 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 145 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 370 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 397 optimal weight: 0.9990 chunk 312 optimal weight: 0.0010 chunk 196 optimal weight: 2.9990 chunk 342 optimal weight: 0.5980 chunk 181 optimal weight: 3.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN A 136 GLN A 246 GLN A 635 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN B 136 GLN B 246 GLN B 635 GLN B 844 GLN ** B 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN ** B 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 136 GLN C 246 GLN C 635 GLN C 844 GLN ** C 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 967 GLN ** C 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN D 136 GLN D 246 GLN D 635 GLN ** D 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 967 GLN ** D 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.144765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.127031 restraints weight = 30994.060| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 0.92 r_work: 0.3305 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33544 Z= 0.123 Angle : 0.550 8.414 45760 Z= 0.288 Chirality : 0.045 0.138 4784 Planarity : 0.004 0.033 6040 Dihedral : 5.942 60.003 4460 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.87 % Favored : 96.93 % Rotamer: Outliers : 1.64 % Allowed : 18.00 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.13), residues: 4040 helix: 0.32 (0.22), residues: 524 sheet: 0.80 (0.14), residues: 1396 loop : -0.10 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 858 TYR 0.023 0.002 TYR B 101 PHE 0.009 0.001 PHE A 990 TRP 0.030 0.002 TRP B 554 HIS 0.003 0.001 HIS D 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (33544) covalent geometry : angle 0.54950 / 0.29 (45760) hydrogen bonds : bond 0.04020 / 2.66 ( 1139) hydrogen bonds : angle 5.20996 / 3.69 ( 3081) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 456 time to evaluate : 1.216 Fit side-chains REVERT: A 3 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6112 (tmt) REVERT: A 244 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7849 (tm-30) REVERT: A 439 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: A 798 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7965 (pt0) REVERT: B 3 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6141 (tmt) REVERT: B 244 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: B 439 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: C 3 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6116 (tmt) REVERT: C 244 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: C 439 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: D 3 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6107 (tmt) REVERT: D 244 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: D 439 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: D 798 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7977 (pt0) outliers start: 57 outliers final: 30 residues processed: 481 average time/residue: 0.8411 time to fit residues: 467.9845 Evaluate side-chains 498 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 454 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 760 ASN Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 662 LYS Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 662 LYS Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 760 ASN Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 798 GLU Chi-restraints excluded: chain D residue 856 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 87 optimal weight: 0.3980 chunk 267 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 318 optimal weight: 0.9980 chunk 390 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 334 optimal weight: 10.0000 chunk 245 optimal weight: 3.9990 chunk 92 optimal weight: 0.0970 chunk 178 optimal weight: 3.9990 chunk 2 optimal weight: 0.0570 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN A 136 GLN A 246 GLN A 635 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN B 136 GLN B 246 GLN B 635 GLN ** B 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN ** B 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 136 GLN C 246 GLN C 635 GLN ** C 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 967 GLN ** C 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN D 136 GLN D 246 GLN D 635 GLN ** D 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 967 GLN ** D 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.147492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130030 restraints weight = 31178.371| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 0.92 r_work: 0.3353 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33544 Z= 0.098 Angle : 0.516 8.290 45760 Z= 0.269 Chirality : 0.043 0.135 4784 Planarity : 0.004 0.032 6040 Dihedral : 5.631 58.199 4460 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.87 % Favored : 96.93 % Rotamer: Outliers : 1.21 % Allowed : 18.55 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.13), residues: 4040 helix: 0.55 (0.23), residues: 524 sheet: 0.83 (0.14), residues: 1396 loop : -0.06 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 858 TYR 0.019 0.001 TYR D 101 PHE 0.007 0.001 PHE C 990 TRP 0.033 0.001 TRP B 554 HIS 0.003 0.001 HIS D 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (33544) covalent geometry : angle 0.51625 / 0.27 (45760) hydrogen bonds : bond 0.03527 / 2.33 ( 1139) hydrogen bonds : angle 5.01043 / 3.55 ( 3081) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8080 Ramachandran restraints generated. 4040 Oldfield, 0 Emsley, 4040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 475 time to evaluate : 1.344 Fit side-chains REVERT: A 3 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6124 (tmt) REVERT: A 439 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: A 637 ILE cc_start: 0.8448 (mt) cc_final: 0.8155 (mt) REVERT: A 798 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7956 (pt0) REVERT: B 368 MET cc_start: 0.8040 (mmp) cc_final: 0.7689 (tpp) REVERT: B 439 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: B 637 ILE cc_start: 0.8445 (mt) cc_final: 0.8155 (mt) REVERT: C 368 MET cc_start: 0.8043 (mmp) cc_final: 0.7682 (tpp) REVERT: C 439 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: C 637 ILE cc_start: 0.8452 (mt) cc_final: 0.8164 (mt) REVERT: D 3 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6119 (tmt) REVERT: D 439 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: D 637 ILE cc_start: 0.8450 (mt) cc_final: 0.8162 (mt) REVERT: D 798 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7946 (pt0) outliers start: 42 outliers final: 23 residues processed: 490 average time/residue: 0.8265 time to fit residues: 469.2567 Evaluate side-chains 502 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 471 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 967 GLN Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 662 LYS Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain C residue 77 CYS Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 662 LYS Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 77 CYS Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 798 GLU Chi-restraints excluded: chain D residue 856 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 296 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 364 optimal weight: 9.9990 chunk 390 optimal weight: 0.4980 chunk 387 optimal weight: 0.8980 chunk 401 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 chunk 339 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 350 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN A 246 GLN A 635 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 GLN ** B 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN ** B 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN C 246 GLN C 635 GLN ** C 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 967 GLN ** C 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN D 246 GLN D 635 GLN ** D 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 967 GLN ** D 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.147362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.129969 restraints weight = 31104.986| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 0.91 r_work: 0.3347 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 33544 Z= 0.135 Angle : 0.631 59.137 45760 Z= 0.352 Chirality : 0.044 0.407 4784 Planarity : 0.004 0.032 6040 Dihedral : 5.569 58.242 4456 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.90 % Favored : 96.91 % Rotamer: Outliers : 1.01 % Allowed : 19.01 % Favored : 79.98 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.13), residues: 4040 helix: 0.51 (0.23), residues: 524 sheet: 0.83 (0.14), residues: 1396 loop : -0.05 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 858 TYR 0.020 0.001 TYR D 101 PHE 0.007 0.001 PHE C 990 TRP 0.031 0.002 TRP B 554 HIS 0.003 0.001 HIS D 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (33544) covalent geometry : angle 0.63069 / 0.35 (45760) hydrogen bonds : bond 0.03556 / 2.35 ( 1139) hydrogen bonds : angle 5.01099 / 3.55 ( 3081) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13126.53 seconds wall clock time: 223 minutes 56.84 seconds (13436.84 seconds total)