Starting phenix.real_space_refine on Sat Feb 7 12:48:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y45_72471/02_2026/9y45_72471.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y45_72471/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9y45_72471/02_2026/9y45_72471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y45_72471/02_2026/9y45_72471.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y45_72471/02_2026/9y45_72471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y45_72471/02_2026/9y45_72471.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 8.81, per 1000 atoms: 0.27 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: 2.46 Conformation dependent library (CDL) restraints added in 1.1 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: 1.62 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: 8.48 Time building geometry restraints manager: 3.45 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: 0.09 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: 8.600 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 32.030 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: 0.010 Load rotamer database and sin/cos tables:9.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 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 covalent geometry : bond 0.00426 (33544) covalent geometry : angle 0.69218 (45760) hydrogen bonds : bond 0.18178 ( 1139) hydrogen bonds : angle 7.28498 ( 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 : 1.234 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: 0.8634 time to fit residues: 496.5257 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 : 1.139 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.142203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124351 restraints weight = 31365.896| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 0.93 r_work: 0.3272 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.0699 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= 0.174 Angle : 0.620 7.365 45760 Z= 0.330 Chirality : 0.047 0.148 4784 Planarity : 0.005 0.043 6040 Dihedral : 6.384 63.828 4467 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.77 % Favored : 97.03 % Rotamer: Outliers : 3.11 % Allowed : 16.22 % Favored : 80.67 % 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 0.029 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 C 647 Details of bonding type rmsd covalent geometry : bond 0.00372 (33544) covalent geometry : angle 0.62027 (45760) hydrogen bonds : bond 0.05434 ( 1139) hydrogen bonds : angle 5.81286 ( 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 593 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 485 time to evaluate : 1.275 Fit side-chains REVERT: A 188 MET cc_start: 0.9069 (ttm) cc_final: 0.8806 (ttp) REVERT: A 439 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: A 738 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7520 (tt) REVERT: A 1014 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7584 (mtm-85) REVERT: B 188 MET cc_start: 0.9075 (ttm) cc_final: 0.8817 (ttp) REVERT: B 439 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: B 738 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7547 (tt) REVERT: B 1014 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7598 (mtm-85) REVERT: C 188 MET cc_start: 0.9074 (ttm) cc_final: 0.8818 (ttp) REVERT: C 439 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: C 738 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7551 (tt) REVERT: C 1014 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7616 (mtm-85) REVERT: D 188 MET cc_start: 0.9071 (ttm) cc_final: 0.8810 (ttp) REVERT: D 439 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: D 738 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7521 (tt) REVERT: D 1014 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7577 (mtm-85) outliers start: 108 outliers final: 35 residues processed: 542 average time/residue: 0.8195 time to fit residues: 513.1274 Evaluate side-chains 518 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 471 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 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 656 MET 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 656 MET 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: 0.9980 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: 2.9990 chunk 114 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 94 HIS A 136 GLN A 164 GLN A 246 GLN A 760 ASN 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 164 GLN B 246 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 164 GLN C 246 GLN C 605 ASN 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 164 GLN D 246 GLN D 605 ASN D 762 GLN D 967 GLN ** D 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.140574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122639 restraints weight = 31199.525| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 0.92 r_work: 0.3249 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 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 : 0.005 0.039 33544 Z= 0.218 Angle : 0.656 7.924 45760 Z= 0.350 Chirality : 0.049 0.239 4784 Planarity : 0.006 0.040 6040 Dihedral : 6.539 64.321 4460 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.22 % Favored : 96.58 % Rotamer: Outliers : 3.20 % Allowed : 16.24 % 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: 0.11 (0.13), residues: 4040 helix: -0.22 (0.22), residues: 536 sheet: 0.59 (0.14), residues: 1312 loop : -0.08 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 858 TYR 0.033 0.003 TYR A 101 PHE 0.016 0.002 PHE D 990 TRP 0.035 0.003 TRP B 554 HIS 0.005 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00475 (33544) covalent geometry : angle 0.65635 (45760) hydrogen bonds : bond 0.05547 ( 1139) hydrogen bonds : angle 5.71538 ( 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 596 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 485 time to evaluate : 1.238 Fit side-chains REVERT: A 3 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6083 (tmt) REVERT: A 235 ASP cc_start: 0.8399 (p0) cc_final: 0.8176 (p0) REVERT: A 244 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7902 (tm-30) REVERT: A 439 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: A 738 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7431 (tt) REVERT: A 904 GLN cc_start: 0.8177 (mt0) cc_final: 0.7309 (pm20) REVERT: A 967 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8642 (tt0) REVERT: B 3 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6142 (tmt) REVERT: B 188 MET cc_start: 0.9051 (ttm) cc_final: 0.8836 (ttp) REVERT: B 235 ASP cc_start: 0.8395 (p0) cc_final: 0.8171 (p0) REVERT: B 439 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: B 738 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7473 (tt) REVERT: B 904 GLN cc_start: 0.8161 (mt0) cc_final: 0.7305 (pm20) REVERT: C 3 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6113 (tmt) REVERT: C 188 MET cc_start: 0.9047 (ttm) cc_final: 0.8833 (ttp) REVERT: C 235 ASP cc_start: 0.8408 (p0) cc_final: 0.8198 (p0) REVERT: C 439 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: C 738 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7500 (tt) REVERT: C 904 GLN cc_start: 0.8161 (mt0) cc_final: 0.7295 (pm20) REVERT: C 967 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8639 (tt0) REVERT: D 3 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6072 (tmt) REVERT: D 188 MET cc_start: 0.9059 (ttm) cc_final: 0.8844 (ttp) REVERT: D 235 ASP cc_start: 0.8396 (p0) cc_final: 0.8162 (p0) REVERT: D 244 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: D 439 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: D 738 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7433 (tt) REVERT: D 769 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7551 (tmt) REVERT: D 904 GLN cc_start: 0.8164 (mt0) cc_final: 0.7304 (pm20) REVERT: D 967 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8645 (tt0) outliers start: 111 outliers final: 45 residues processed: 537 average time/residue: 0.8436 time to fit residues: 522.2564 Evaluate side-chains 537 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 474 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 83 ASP Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 190 LEU 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 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 190 LEU 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 656 MET 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 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 190 LEU 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 656 MET 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 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 83 ASP 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 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: 5.9990 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 214 optimal weight: 8.9990 chunk 151 optimal weight: 0.7980 chunk 339 optimal weight: 5.9990 chunk 227 optimal weight: 0.4980 chunk 327 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 136 GLN A 164 GLN A 246 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 164 GLN B 246 GLN B 891 GLN B 967 GLN ** B 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 136 GLN C 164 GLN C 246 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 164 GLN D 246 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 = 0.3578 r_free = 0.3578 target = 0.142248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124468 restraints weight = 31052.154| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 0.92 r_work: 0.3274 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33544 Z= 0.163 Angle : 0.595 7.251 45760 Z= 0.316 Chirality : 0.046 0.182 4784 Planarity : 0.005 0.036 6040 Dihedral : 6.310 63.109 4460 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.82 % Favored : 96.98 % Rotamer: Outliers : 2.36 % Allowed : 17.11 % 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: 0.23 (0.13), residues: 4040 helix: 0.08 (0.22), residues: 512 sheet: 0.68 (0.13), residues: 1396 loop : -0.09 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 858 TYR 0.027 0.002 TYR B 101 PHE 0.012 0.002 PHE D 990 TRP 0.033 0.002 TRP B 554 HIS 0.004 0.001 HIS C 647 Details of bonding type rmsd covalent geometry : bond 0.00349 (33544) covalent geometry : angle 0.59495 (45760) hydrogen bonds : bond 0.04743 ( 1139) hydrogen bonds : angle 5.52548 ( 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 567 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 485 time to evaluate : 1.260 Fit side-chains REVERT: A 3 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6095 (tmt) REVERT: A 439 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: A 798 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8061 (pt0) REVERT: A 904 GLN cc_start: 0.8169 (mt0) cc_final: 0.7309 (pm20) REVERT: B 3 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6133 (tmt) REVERT: B 439 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: B 798 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8065 (pt0) REVERT: B 904 GLN cc_start: 0.8162 (mt0) cc_final: 0.7318 (pm20) REVERT: B 967 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8644 (tt0) REVERT: C 3 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6106 (tmt) REVERT: C 439 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: C 798 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: C 904 GLN cc_start: 0.8160 (mt0) cc_final: 0.7307 (pm20) REVERT: D 3 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6108 (tmt) REVERT: D 439 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: D 738 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7433 (tt) REVERT: D 798 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8062 (pt0) REVERT: D 904 GLN cc_start: 0.8167 (mt0) cc_final: 0.7315 (pm20) outliers start: 82 outliers final: 31 residues processed: 517 average time/residue: 0.8032 time to fit residues: 478.8289 Evaluate side-chains 508 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 463 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 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 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 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 656 MET 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 B residue 967 GLN Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 77 CYS 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 547 LEU Chi-restraints excluded: chain C residue 656 MET 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 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 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: 5.9990 chunk 158 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 300 optimal weight: 0.3980 chunk 47 optimal weight: 0.3980 chunk 367 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 136 GLN A 246 GLN A 635 GLN A 762 GLN A 967 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN B 136 GLN B 246 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 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.144199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.126575 restraints weight = 31233.633| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 0.92 r_work: 0.3298 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1091 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= 0.124 Angle : 0.551 7.223 45760 Z= 0.291 Chirality : 0.045 0.156 4784 Planarity : 0.004 0.034 6040 Dihedral : 6.024 61.626 4460 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.82 % Favored : 96.98 % Rotamer: Outliers : 2.28 % Allowed : 17.31 % Favored : 80.41 % 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: 0.31 (0.13), residues: 4040 helix: 0.20 (0.22), residues: 524 sheet: 0.75 (0.14), residues: 1388 loop : -0.07 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 858 TYR 0.023 0.002 TYR B 101 PHE 0.009 0.001 PHE D 990 TRP 0.030 0.002 TRP B 554 HIS 0.003 0.001 HIS A 647 Details of bonding type rmsd covalent geometry : bond 0.00259 (33544) covalent geometry : angle 0.55084 (45760) hydrogen bonds : bond 0.04155 ( 1139) hydrogen bonds : angle 5.31626 ( 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 555 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 476 time to evaluate : 1.166 Fit side-chains REVERT: A 3 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6075 (tmt) REVERT: A 244 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: A 439 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: A 642 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8268 (mt-10) REVERT: A 798 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8054 (pt0) REVERT: A 1014 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7559 (mtm-85) REVERT: B 3 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6098 (tmt) REVERT: B 244 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: B 439 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: B 642 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8268 (mt-10) REVERT: B 798 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8070 (pt0) REVERT: C 3 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6069 (tmt) REVERT: C 244 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: C 439 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: C 642 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8242 (mt-10) REVERT: C 798 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8065 (pt0) REVERT: D 3 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6062 (tmt) REVERT: D 244 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: D 439 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: D 642 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8263 (mt-10) REVERT: D 798 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8056 (pt0) REVERT: D 1014 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7558 (mtm-85) outliers start: 79 outliers final: 28 residues processed: 515 average time/residue: 0.7536 time to fit residues: 447.5575 Evaluate side-chains 510 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 466 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 244 GLU 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 656 MET 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 391 SER Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 656 MET 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 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 662 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 283 optimal weight: 0.7980 chunk 383 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 362 optimal weight: 3.9990 chunk 361 optimal weight: 0.9990 chunk 262 optimal weight: 1.9990 chunk 397 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 327 optimal weight: 0.6980 chunk 289 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3595 r_free = 0.3595 target = 0.143694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.126031 restraints weight = 31079.849| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 0.92 r_work: 0.3292 rms_B_bonded: 1.26 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: 0.8623 moved from start: 0.1103 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= 0.138 Angle : 0.564 7.497 45760 Z= 0.297 Chirality : 0.045 0.151 4784 Planarity : 0.004 0.033 6040 Dihedral : 6.047 61.788 4460 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.72 % Favored : 97.08 % Rotamer: Outliers : 1.96 % Allowed : 17.19 % Favored : 80.85 % 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: 0.24 (0.22), residues: 524 sheet: 0.78 (0.14), residues: 1388 loop : -0.07 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 858 TYR 0.026 0.002 TYR A 101 PHE 0.010 0.001 PHE C 990 TRP 0.030 0.002 TRP B 554 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00294 (33544) covalent geometry : angle 0.56376 (45760) hydrogen bonds : bond 0.04264 ( 1139) hydrogen bonds : angle 5.28734 ( 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 539 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 471 time to evaluate : 1.296 Fit side-chains REVERT: A 3 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6105 (tmt) REVERT: A 244 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: A 439 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: A 642 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8288 (mt-10) REVERT: A 798 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8042 (pt0) REVERT: A 1014 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7666 (mtm-85) REVERT: B 3 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6141 (tmt) REVERT: B 244 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: B 439 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: B 642 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8257 (mt-10) REVERT: B 798 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8062 (pt0) REVERT: C 3 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6112 (tmt) REVERT: C 244 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: C 439 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: C 798 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8056 (pt0) REVERT: D 3 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6085 (tmt) REVERT: D 244 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: D 439 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: D 642 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8281 (mt-10) REVERT: D 798 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: D 1014 ARG cc_start: 0.7916 (mtm-85) cc_final: 0.7666 (mtm-85) outliers start: 68 outliers final: 38 residues processed: 501 average time/residue: 0.7970 time to fit residues: 458.8570 Evaluate side-chains 519 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 465 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 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 662 LYS 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 244 GLU 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 656 MET Chi-restraints excluded: chain B residue 662 LYS Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 767 SER 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 B residue 967 GLN 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 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 656 MET 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 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 662 LYS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 68 optimal weight: 7.9990 chunk 301 optimal weight: 4.9990 chunk 304 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 305 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 351 optimal weight: 3.9990 chunk 348 optimal weight: 0.6980 chunk 387 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 221 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 760 ASN D 967 GLN ** D 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.123102 restraints weight = 31116.585| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 0.92 r_work: 0.3255 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 33544 Z= 0.219 Angle : 0.646 8.001 45760 Z= 0.342 Chirality : 0.049 0.164 4784 Planarity : 0.005 0.038 6040 Dihedral : 6.433 62.632 4460 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.24 % Favored : 96.56 % Rotamer: Outliers : 2.59 % Allowed : 16.68 % Favored : 80.73 % 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: 0.26 (0.13), residues: 4040 helix: 0.09 (0.22), residues: 512 sheet: 0.77 (0.14), residues: 1356 loop : -0.11 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 858 TYR 0.034 0.003 TYR B 101 PHE 0.016 0.002 PHE C 990 TRP 0.034 0.003 TRP B 554 HIS 0.005 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00483 (33544) covalent geometry : angle 0.64629 (45760) hydrogen bonds : bond 0.05151 ( 1139) hydrogen bonds : angle 5.50014 ( 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 561 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 471 time to evaluate : 1.079 Fit side-chains REVERT: A 3 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6187 (tmt) REVERT: A 244 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: A 335 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8645 (tt0) REVERT: A 439 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: A 738 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7457 (tt) REVERT: A 769 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7560 (tmt) REVERT: A 798 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8010 (pt0) REVERT: A 904 GLN cc_start: 0.8188 (mt0) cc_final: 0.7322 (pm20) REVERT: B 3 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6191 (tmt) REVERT: B 244 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7869 (tm-30) REVERT: B 335 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8645 (tt0) REVERT: B 439 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: B 738 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7465 (tt) REVERT: B 769 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7545 (tmt) REVERT: B 904 GLN cc_start: 0.8183 (mt0) cc_final: 0.7325 (pm20) REVERT: C 3 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6172 (tmt) REVERT: C 244 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7849 (tm-30) REVERT: C 335 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8652 (tt0) REVERT: C 439 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: C 738 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7472 (tt) REVERT: C 769 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7542 (tmt) REVERT: C 904 GLN cc_start: 0.8183 (mt0) cc_final: 0.7317 (pm20) REVERT: D 3 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6197 (tmt) REVERT: D 244 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: D 335 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: D 439 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: D 798 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8019 (pt0) REVERT: D 904 GLN cc_start: 0.8184 (mt0) cc_final: 0.7321 (pm20) outliers start: 90 outliers final: 40 residues processed: 515 average time/residue: 0.8141 time to fit residues: 481.4568 Evaluate side-chains 524 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 460 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 335 GLU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 760 ASN Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 769 MET 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 231 ARG 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 656 MET 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 769 MET 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 190 LEU Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 244 GLU 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 656 MET 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 769 MET 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 314 VAL 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 662 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 223 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 315 optimal weight: 7.9990 chunk 335 optimal weight: 0.3980 chunk 198 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 345 optimal weight: 0.0670 chunk 177 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 225 optimal weight: 0.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 136 GLN C 246 GLN C 635 GLN C 762 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 = 0.3611 r_free = 0.3611 target = 0.145008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.127440 restraints weight = 31202.935| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 0.92 r_work: 0.3301 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1219 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= 0.115 Angle : 0.541 8.204 45760 Z= 0.284 Chirality : 0.044 0.136 4784 Planarity : 0.004 0.034 6040 Dihedral : 5.914 59.886 4460 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.87 % Favored : 96.93 % Rotamer: Outliers : 1.67 % Allowed : 17.97 % 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: 0.29 (0.22), residues: 524 sheet: 0.81 (0.14), residues: 1396 loop : -0.10 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 858 TYR 0.021 0.001 TYR D 101 PHE 0.009 0.001 PHE B 990 TRP 0.032 0.002 TRP B 554 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00239 (33544) covalent geometry : angle 0.54086 (45760) hydrogen bonds : bond 0.03911 ( 1139) hydrogen bonds : angle 5.18253 ( 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 525 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 467 time to evaluate : 1.361 Fit side-chains REVERT: A 3 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6098 (tmt) REVERT: A 439 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: A 798 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8050 (pt0) REVERT: B 3 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6125 (tmt) REVERT: B 439 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: B 769 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7565 (tmt) REVERT: C 3 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6096 (tmt) REVERT: C 439 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: C 769 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7560 (tmt) REVERT: D 3 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6108 (tmt) REVERT: D 439 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: D 798 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8058 (pt0) outliers start: 58 outliers final: 22 residues processed: 486 average time/residue: 0.7751 time to fit residues: 433.3656 Evaluate side-chains 499 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 465 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 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 656 MET Chi-restraints excluded: chain B residue 662 LYS 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 439 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 656 MET Chi-restraints excluded: chain C residue 662 LYS Chi-restraints excluded: chain C residue 769 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 145 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 370 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 397 optimal weight: 0.8980 chunk 312 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 342 optimal weight: 0.0980 chunk 181 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 635 GLN ** B 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.124650 restraints weight = 31062.859| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 0.92 r_work: 0.3275 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1112 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= 0.171 Angle : 0.597 8.429 45760 Z= 0.314 Chirality : 0.046 0.146 4784 Planarity : 0.005 0.035 6040 Dihedral : 6.184 61.680 4460 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.97 % Favored : 96.83 % Rotamer: Outliers : 1.70 % Allowed : 18.12 % 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: 0.35 (0.13), residues: 4040 helix: 0.25 (0.22), residues: 512 sheet: 0.81 (0.14), residues: 1396 loop : -0.09 (0.13), residues: 2132 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 B 990 TRP 0.031 0.002 TRP B 554 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00370 (33544) covalent geometry : angle 0.59718 (45760) hydrogen bonds : bond 0.04615 ( 1139) hydrogen bonds : angle 5.31996 ( 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 524 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 465 time to evaluate : 1.317 Fit side-chains REVERT: A 3 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6165 (tmt) REVERT: A 335 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: A 439 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: A 769 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7584 (tmt) REVERT: A 798 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8038 (pt0) REVERT: B 3 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6174 (tmt) REVERT: B 335 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: B 439 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: B 769 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7580 (tmt) REVERT: C 3 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6155 (tmt) REVERT: C 335 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8629 (tt0) REVERT: C 439 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: C 769 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7590 (tmt) REVERT: D 3 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6159 (tmt) REVERT: D 335 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8623 (tt0) REVERT: D 439 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: D 798 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8046 (pt0) outliers start: 59 outliers final: 31 residues processed: 493 average time/residue: 0.8832 time to fit residues: 499.1854 Evaluate side-chains 515 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 467 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 314 VAL Chi-restraints excluded: chain A residue 335 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 769 MET 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 335 GLU 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 656 MET Chi-restraints excluded: chain B residue 662 LYS 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 335 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 656 MET Chi-restraints excluded: chain C residue 662 LYS Chi-restraints excluded: chain C residue 769 MET 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 125 SER Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 335 GLU 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 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: 7.9990 chunk 267 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 318 optimal weight: 0.2980 chunk 390 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 334 optimal weight: 7.9990 chunk 245 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 246 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN B 246 GLN B 635 GLN B 844 GLN ** B 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 844 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.126231 restraints weight = 31220.740| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 0.92 r_work: 0.3296 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33544 Z= 0.133 Angle : 0.562 8.482 45760 Z= 0.295 Chirality : 0.045 0.141 4784 Planarity : 0.004 0.034 6040 Dihedral : 6.014 59.875 4460 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.90 % Favored : 96.91 % Rotamer: Outliers : 1.32 % Allowed : 18.49 % 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: 0.33 (0.13), residues: 4040 helix: 0.23 (0.22), residues: 524 sheet: 0.81 (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 B 858 TYR 0.024 0.002 TYR C 101 PHE 0.010 0.001 PHE B 990 TRP 0.029 0.002 TRP B 554 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00284 (33544) covalent geometry : angle 0.56182 (45760) hydrogen bonds : bond 0.04163 ( 1139) hydrogen bonds : angle 5.19863 ( 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 507 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 461 time to evaluate : 1.178 Fit side-chains REVERT: A 3 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6160 (tmt) REVERT: A 439 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: A 769 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7576 (tmt) REVERT: A 798 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7960 (pt0) REVERT: B 3 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6146 (tmt) REVERT: B 244 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: B 439 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: B 769 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7569 (tmt) REVERT: C 3 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6117 (tmt) REVERT: C 439 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: C 769 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7583 (tmt) REVERT: D 3 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6159 (tmt) REVERT: D 244 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: D 439 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: D 798 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7969 (pt0) outliers start: 46 outliers final: 28 residues processed: 476 average time/residue: 0.8927 time to fit residues: 486.0493 Evaluate side-chains 507 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 464 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 769 MET 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 391 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 662 LYS 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 391 SER Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 656 MET Chi-restraints excluded: chain C residue 662 LYS Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 769 MET 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 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: 0.9980 chunk 364 optimal weight: 2.9990 chunk 390 optimal weight: 7.9990 chunk 387 optimal weight: 0.6980 chunk 401 optimal weight: 0.9990 chunk 271 optimal weight: 2.9990 chunk 339 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 350 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 246 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN B 246 GLN B 635 GLN B 844 GLN ** B 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN C 246 GLN C 635 GLN C 762 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 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.143727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126013 restraints weight = 31098.323| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 0.92 r_work: 0.3292 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33544 Z= 0.138 Angle : 0.568 8.445 45760 Z= 0.298 Chirality : 0.045 0.142 4784 Planarity : 0.004 0.033 6040 Dihedral : 6.014 59.509 4460 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.82 % Favored : 96.98 % Rotamer: Outliers : 1.44 % Allowed : 18.35 % Favored : 80.21 % 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: 0.21 (0.22), residues: 524 sheet: 0.82 (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 B 858 TYR 0.025 0.002 TYR C 101 PHE 0.011 0.001 PHE C 990 TRP 0.029 0.002 TRP B 554 HIS 0.004 0.001 HIS D 217 Details of bonding type rmsd covalent geometry : bond 0.00295 (33544) covalent geometry : angle 0.56765 (45760) hydrogen bonds : bond 0.04241 ( 1139) hydrogen bonds : angle 5.19360 ( 3081) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13299.83 seconds wall clock time: 226 minutes 59.11 seconds (13619.11 seconds total)