Starting phenix.real_space_refine on Wed Oct 28 10:15:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y5l_72512/10_2026/9y5l_72512.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y5l_72512/10_2026/9y5l_72512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y5l_72512/10_2026/9y5l_72512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y5l_72512/10_2026/9y5l_72512.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y5l_72512/10_2026/9y5l_72512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y5l_72512/10_2026/9y5l_72512.map" } resolution = 2.91 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= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 183 5.16 5 C 17496 2.51 5 N 4518 2.21 5 O 5253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27450 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "B" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "C" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Time building chain proxies: 6.42, per 1000 atoms: 0.23 Number of scatterers: 27450 At special positions: 0 Unit cell: (154, 154, 166.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 183 16.00 O 5253 8.00 N 4518 7.00 C 17496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 197 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.04 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.04 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS A 748 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 826 " - pdb=" SG CYS A 848 " distance=2.04 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 837 " distance=2.03 Simple disulfide: pdb=" SG CYS A 938 " - pdb=" SG CYS A 949 " distance=2.03 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1137 " distance=2.04 Simple disulfide: pdb=" SG CYS A1176 " - pdb=" SG CYS A1221 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 614 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 597 " distance=2.04 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.03 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 748 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 826 " - pdb=" SG CYS B 848 " distance=2.04 Simple disulfide: pdb=" SG CYS B 831 " - pdb=" SG CYS B 837 " distance=2.03 Simple disulfide: pdb=" SG CYS B 938 " - pdb=" SG CYS B 949 " distance=2.03 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1137 " distance=2.03 Simple disulfide: pdb=" SG CYS B1176 " - pdb=" SG CYS B1221 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 197 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 256 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 300 " distance=2.03 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 614 " distance=2.03 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 499 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 548 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 578 " distance=2.03 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 597 " distance=2.04 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 683 " distance=2.03 Simple disulfide: pdb=" SG CYS C 708 " - pdb=" SG CYS C 733 " distance=2.03 Simple disulfide: pdb=" SG CYS C 748 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 826 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C 831 " - pdb=" SG CYS C 837 " distance=2.03 Simple disulfide: pdb=" SG CYS C 938 " - pdb=" SG CYS C 949 " distance=2.03 Simple disulfide: pdb=" SG CYS C1126 " - pdb=" SG CYS C1137 " distance=2.03 Simple disulfide: pdb=" SG CYS C1176 " - pdb=" SG CYS C1221 " distance=2.03 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: 2.11 Conformation dependent library (CDL) restraints added in 975.4 milliseconds 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6588 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 74 sheets defined 25.3% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 89 through 92 removed outlier: 3.889A pdb=" N LYS A 92 " --> pdb=" O LEU A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 371 through 379 removed outlier: 3.558A pdb=" N LEU A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 removed outlier: 4.042A pdb=" N ILE A 394 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.917A pdb=" N PHE A 464 " --> pdb=" O TRP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 568 through 571 removed outlier: 3.743A pdb=" N CYS A 571 " --> pdb=" O SER A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 568 through 571' Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 707 through 715 Processing helix chain 'A' and resid 825 through 831 Processing helix chain 'A' and resid 834 through 840 removed outlier: 3.814A pdb=" N GLN A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 843 No H-bonds generated for 'chain 'A' and resid 841 through 843' Processing helix chain 'A' and resid 844 through 874 removed outlier: 3.879A pdb=" N CYS A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 886 removed outlier: 3.512A pdb=" N ASP A 885 " --> pdb=" O LYS A 882 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 886 " --> pdb=" O LEU A 883 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 882 through 886' Processing helix chain 'A' and resid 914 through 923 removed outlier: 4.440A pdb=" N LYS A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 936 Processing helix chain 'A' and resid 946 through 954 Processing helix chain 'A' and resid 964 through 977 Processing helix chain 'A' and resid 991 through 1002 removed outlier: 3.623A pdb=" N GLY A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1011 removed outlier: 3.741A pdb=" N LEU A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1030 removed outlier: 3.529A pdb=" N ILE A1017 " --> pdb=" O ASN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1058 Processing helix chain 'A' and resid 1059 through 1062 removed outlier: 3.657A pdb=" N ASN A1062 " --> pdb=" O GLN A1059 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1059 through 1062' Processing helix chain 'A' and resid 1070 through 1078 Processing helix chain 'A' and resid 1079 through 1127 removed outlier: 4.271A pdb=" N ALA A1085 " --> pdb=" O LEU A1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 removed outlier: 3.879A pdb=" N LYS B 92 " --> pdb=" O LEU B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 92' Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 344 through 350 removed outlier: 3.731A pdb=" N TRP B 348 " --> pdb=" O ASN B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 379 removed outlier: 3.570A pdb=" N LEU B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 removed outlier: 4.050A pdb=" N ILE B 394 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 458 through 464 removed outlier: 3.779A pdb=" N PHE B 464 " --> pdb=" O TRP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 707 through 715 Processing helix chain 'B' and resid 825 through 831 Processing helix chain 'B' and resid 834 through 841 removed outlier: 3.736A pdb=" N GLN B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 874 removed outlier: 3.894A pdb=" N CYS B 848 " --> pdb=" O TYR B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 886 removed outlier: 3.691A pdb=" N GLY B 886 " --> pdb=" O LEU B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 923 removed outlier: 4.434A pdb=" N LYS B 923 " --> pdb=" O LEU B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 936 Processing helix chain 'B' and resid 946 through 954 Processing helix chain 'B' and resid 964 through 977 Processing helix chain 'B' and resid 991 through 1002 removed outlier: 3.614A pdb=" N GLY B1002 " --> pdb=" O TYR B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1011 removed outlier: 3.759A pdb=" N LEU B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1030 Processing helix chain 'B' and resid 1036 through 1058 Processing helix chain 'B' and resid 1059 through 1062 removed outlier: 3.629A pdb=" N ASN B1062 " --> pdb=" O GLN B1059 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1059 through 1062' Processing helix chain 'B' and resid 1070 through 1078 Processing helix chain 'B' and resid 1079 through 1127 removed outlier: 4.265A pdb=" N ALA B1085 " --> pdb=" O LEU B1081 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B1125 " --> pdb=" O GLU B1121 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B1127 " --> pdb=" O VAL B1123 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1215 removed outlier: 3.821A pdb=" N ASN B1214 " --> pdb=" O THR B1211 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL B1215 " --> pdb=" O GLU B1212 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1211 through 1215' Processing helix chain 'C' and resid 89 through 92 removed outlier: 3.850A pdb=" N LYS C 92 " --> pdb=" O LEU C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 293 through 303 Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 371 through 379 removed outlier: 3.583A pdb=" N LEU C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 394 removed outlier: 4.022A pdb=" N ILE C 394 " --> pdb=" O ALA C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 424 through 429 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 458 through 464 removed outlier: 3.949A pdb=" N PHE C 464 " --> pdb=" O TRP C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 568 through 571 removed outlier: 3.790A pdb=" N CYS C 571 " --> pdb=" O SER C 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 568 through 571' Processing helix chain 'C' and resid 579 through 581 No H-bonds generated for 'chain 'C' and resid 579 through 581' Processing helix chain 'C' and resid 707 through 715 Processing helix chain 'C' and resid 825 through 831 Processing helix chain 'C' and resid 834 through 840 removed outlier: 3.825A pdb=" N GLN C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 843 No H-bonds generated for 'chain 'C' and resid 841 through 843' Processing helix chain 'C' and resid 844 through 874 removed outlier: 3.920A pdb=" N CYS C 848 " --> pdb=" O TYR C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 923 removed outlier: 4.440A pdb=" N LYS C 923 " --> pdb=" O LEU C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 936 Processing helix chain 'C' and resid 946 through 954 Processing helix chain 'C' and resid 964 through 977 Processing helix chain 'C' and resid 991 through 1002 removed outlier: 3.586A pdb=" N GLY C1002 " --> pdb=" O TYR C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1011 removed outlier: 3.712A pdb=" N LEU C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1030 Processing helix chain 'C' and resid 1036 through 1058 Processing helix chain 'C' and resid 1059 through 1062 removed outlier: 3.684A pdb=" N ASN C1062 " --> pdb=" O GLN C1059 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1059 through 1062' Processing helix chain 'C' and resid 1070 through 1078 Processing helix chain 'C' and resid 1079 through 1127 removed outlier: 4.254A pdb=" N ALA C1085 " --> pdb=" O LEU C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1211 through 1215 removed outlier: 3.800A pdb=" N ASN C1214 " --> pdb=" O THR C1211 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL C1215 " --> pdb=" O GLU C1212 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1211 through 1215' Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.516A pdb=" N SER A 37 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TYR A 75 " --> pdb=" O SER A 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 68 removed outlier: 3.574A pdb=" N THR A 60 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN A 286 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 8.657A pdb=" N THR A 255 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR A 174 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N TRP A 188 " --> pdb=" O CYS A 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 98 removed outlier: 4.195A pdb=" N GLY A 157 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR A 205 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 241 removed outlier: 5.164A pdb=" N PHE A 236 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N PHE A 227 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 238 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 222 " --> pdb=" O GLU A 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 313 Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.554A pdb=" N GLY A 686 " --> pdb=" O TYR A 325 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 331 through 335 removed outlier: 3.639A pdb=" N GLY A 640 " --> pdb=" O TYR A 633 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 355 Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 365 removed outlier: 3.623A pdb=" N GLU A 361 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER A 438 " --> pdb=" O CYS A 386 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N CYS A 386 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN A 440 " --> pdb=" O PHE A 384 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE A 384 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR A 442 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AB5, first strand: chain 'A' and resid 484 through 488 Processing sheet with id=AB6, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AB7, first strand: chain 'A' and resid 520 through 521 Processing sheet with id=AB8, first strand: chain 'A' and resid 565 through 566 Processing sheet with id=AB9, first strand: chain 'A' and resid 644 through 646 removed outlier: 5.633A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 668 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 738 through 745 removed outlier: 11.085A pdb=" N TYR A 774 " --> pdb=" O ASN A 739 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N THR A 741 " --> pdb=" O TYR A 774 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N PHE A 776 " --> pdb=" O THR A 741 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE A 743 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR A 756 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU A 750 " --> pdb=" O VAL A 758 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 785 through 787 removed outlier: 5.714A pdb=" N ASN A 785 " --> pdb=" O LEU B 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 798 through 816 removed outlier: 6.344A pdb=" N LYS A1165 " --> pdb=" O SER A 804 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE A 806 " --> pdb=" O PRO A1163 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE A 808 " --> pdb=" O TYR A1161 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR A1161 " --> pdb=" O ILE A 808 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A 810 " --> pdb=" O PHE A1159 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE A1159 " --> pdb=" O ASN A 810 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL A 812 " --> pdb=" O ILE A1157 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A1157 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE A 814 " --> pdb=" O TYR A1155 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR A1155 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN A 816 " --> pdb=" O GLY A1153 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY A1153 " --> pdb=" O GLN A 816 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A1153 " --> pdb=" O ALA A1150 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A1144 " --> pdb=" O PHE A1159 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR A1161 " --> pdb=" O HIS A1142 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N HIS A1142 " --> pdb=" O TYR A1161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 798 through 816 removed outlier: 6.344A pdb=" N LYS A1165 " --> pdb=" O SER A 804 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE A 806 " --> pdb=" O PRO A1163 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE A 808 " --> pdb=" O TYR A1161 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR A1161 " --> pdb=" O ILE A 808 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A 810 " --> pdb=" O PHE A1159 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE A1159 " --> pdb=" O ASN A 810 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL A 812 " --> pdb=" O ILE A1157 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A1157 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE A 814 " --> pdb=" O TYR A1155 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR A1155 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN A 816 " --> pdb=" O GLY A1153 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY A1153 " --> pdb=" O GLN A 816 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG A1170 " --> pdb=" O ASN A1192 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN A1192 " --> pdb=" O ARG A1170 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 821 through 824 removed outlier: 4.581A pdb=" N LYS A 821 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 878 through 880 Processing sheet with id=AC7, first strand: chain 'A' and resid 890 through 891 Processing sheet with id=AC8, first strand: chain 'A' and resid 1175 through 1176 Processing sheet with id=AC9, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AD1, first strand: chain 'B' and resid 36 through 40 removed outlier: 5.454A pdb=" N TYR B 75 " --> pdb=" O SER B 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 61 through 68 removed outlier: 3.962A pdb=" N ASN B 286 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 81 through 82 removed outlier: 8.749A pdb=" N THR B 255 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR B 174 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N TRP B 188 " --> pdb=" O CYS B 169 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AD5, first strand: chain 'B' and resid 235 through 241 removed outlier: 5.220A pdb=" N PHE B 236 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N PHE B 227 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 238 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AD7, first strand: chain 'B' and resid 310 through 313 Processing sheet with id=AD8, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AD9, first strand: chain 'B' and resid 331 through 335 removed outlier: 3.614A pdb=" N GLY B 640 " --> pdb=" O TYR B 633 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 354 through 355 removed outlier: 6.934A pdb=" N VAL B 354 " --> pdb=" O SER B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.577A pdb=" N GLU B 361 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 438 " --> pdb=" O ASN B 387 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 383 " --> pdb=" O TYR B 442 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 369 through 370 removed outlier: 3.511A pdb=" N PHE B 370 " --> pdb=" O CYS B 614 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 484 through 488 Processing sheet with id=AE5, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AE6, first strand: chain 'B' and resid 520 through 521 Processing sheet with id=AE7, first strand: chain 'B' and resid 565 through 566 Processing sheet with id=AE8, first strand: chain 'B' and resid 644 through 646 removed outlier: 5.555A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY B 668 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 738 through 745 removed outlier: 10.985A pdb=" N TYR B 774 " --> pdb=" O ASN B 739 " (cutoff:3.500A) removed outlier: 10.086A pdb=" N THR B 741 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N PHE B 776 " --> pdb=" O THR B 741 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE B 743 " --> pdb=" O PHE B 776 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR B 756 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU B 750 " --> pdb=" O VAL B 758 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 785 through 787 removed outlier: 5.715A pdb=" N ASN B 785 " --> pdb=" O LEU C 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'B' and resid 798 through 816 removed outlier: 6.338A pdb=" N LYS B1165 " --> pdb=" O SER B 804 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE B 806 " --> pdb=" O PRO B1163 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE B 808 " --> pdb=" O TYR B1161 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N TYR B1161 " --> pdb=" O ILE B 808 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN B 810 " --> pdb=" O PHE B1159 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE B1159 " --> pdb=" O ASN B 810 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 812 " --> pdb=" O ILE B1157 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B1157 " --> pdb=" O VAL B 812 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE B 814 " --> pdb=" O TYR B1155 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR B1155 " --> pdb=" O PHE B 814 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN B 816 " --> pdb=" O GLY B1153 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY B1153 " --> pdb=" O GLN B 816 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B1153 " --> pdb=" O ALA B1150 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B1144 " --> pdb=" O PHE B1159 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR B1161 " --> pdb=" O HIS B1142 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N HIS B1142 " --> pdb=" O TYR B1161 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 798 through 816 removed outlier: 6.338A pdb=" N LYS B1165 " --> pdb=" O SER B 804 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE B 806 " --> pdb=" O PRO B1163 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE B 808 " --> pdb=" O TYR B1161 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N TYR B1161 " --> pdb=" O ILE B 808 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN B 810 " --> pdb=" O PHE B1159 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE B1159 " --> pdb=" O ASN B 810 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 812 " --> pdb=" O ILE B1157 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B1157 " --> pdb=" O VAL B 812 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE B 814 " --> pdb=" O TYR B1155 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR B1155 " --> pdb=" O PHE B 814 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN B 816 " --> pdb=" O GLY B1153 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY B1153 " --> pdb=" O GLN B 816 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG B1170 " --> pdb=" O ASN B1192 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN B1192 " --> pdb=" O ARG B1170 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 821 through 824 removed outlier: 4.622A pdb=" N LYS B 821 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 890 through 891 Processing sheet with id=AF6, first strand: chain 'B' and resid 1175 through 1176 removed outlier: 3.523A pdb=" N LEU B1175 " --> pdb=" O ILE B1183 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AF8, first strand: chain 'C' and resid 36 through 40 removed outlier: 3.536A pdb=" N SER C 37 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TYR C 75 " --> pdb=" O SER C 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'C' and resid 60 through 68 removed outlier: 3.610A pdb=" N THR C 60 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN C 286 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.585A pdb=" N GLY C 82 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR C 255 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N THR C 174 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N TRP C 188 " --> pdb=" O CYS C 169 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AG3, first strand: chain 'C' and resid 235 through 241 removed outlier: 5.133A pdb=" N PHE C 236 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N PHE C 227 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE C 238 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AG5, first strand: chain 'C' and resid 310 through 313 Processing sheet with id=AG6, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AG7, first strand: chain 'C' and resid 331 through 335 removed outlier: 4.106A pdb=" N ALA C 331 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 640 " --> pdb=" O TYR C 633 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N TYR C 667 " --> pdb=" O ILE C 680 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY C 668 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 354 through 355 removed outlier: 7.032A pdb=" N VAL C 354 " --> pdb=" O SER C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'C' and resid 361 through 365 removed outlier: 3.642A pdb=" N GLU C 361 " --> pdb=" O LYS C 406 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER C 401 " --> pdb=" O HIS C 606 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER C 438 " --> pdb=" O CYS C 386 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N CYS C 386 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN C 440 " --> pdb=" O PHE C 384 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE C 384 " --> pdb=" O GLN C 440 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TYR C 442 " --> pdb=" O ASP C 382 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 369 through 370 Processing sheet with id=AH2, first strand: chain 'C' and resid 484 through 488 Processing sheet with id=AH3, first strand: chain 'C' and resid 492 through 493 Processing sheet with id=AH4, first strand: chain 'C' and resid 520 through 521 Processing sheet with id=AH5, first strand: chain 'C' and resid 565 through 566 Processing sheet with id=AH6, first strand: chain 'C' and resid 738 through 745 removed outlier: 11.024A pdb=" N TYR C 774 " --> pdb=" O ASN C 739 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N THR C 741 " --> pdb=" O TYR C 774 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N PHE C 776 " --> pdb=" O THR C 741 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE C 743 " --> pdb=" O PHE C 776 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR C 756 " --> pdb=" O VAL C 752 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU C 750 " --> pdb=" O VAL C 758 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 798 through 816 removed outlier: 6.805A pdb=" N GLU C 799 " --> pdb=" O ARG C1170 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ARG C1170 " --> pdb=" O GLU C 799 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN C 801 " --> pdb=" O THR C1168 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR C1168 " --> pdb=" O GLN C 801 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR C1166 " --> pdb=" O PRO C 803 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLU C 805 " --> pdb=" O THR C1164 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C1153 " --> pdb=" O ALA C1150 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C1144 " --> pdb=" O PHE C1159 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR C1161 " --> pdb=" O HIS C1142 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS C1142 " --> pdb=" O TYR C1161 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 798 through 816 removed outlier: 6.805A pdb=" N GLU C 799 " --> pdb=" O ARG C1170 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ARG C1170 " --> pdb=" O GLU C 799 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN C 801 " --> pdb=" O THR C1168 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR C1168 " --> pdb=" O GLN C 801 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR C1166 " --> pdb=" O PRO C 803 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLU C 805 " --> pdb=" O THR C1164 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ARG C1170 " --> pdb=" O ASN C1192 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASN C1192 " --> pdb=" O ARG C1170 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 821 through 824 removed outlier: 4.601A pdb=" N LYS C 821 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 890 through 891 Processing sheet with id=AI2, first strand: chain 'C' and resid 1175 through 1176 1057 hydrogen bonds defined for protein. 2931 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: 7.37 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8817 1.34 - 1.47: 6910 1.47 - 1.59: 12113 1.59 - 1.71: 0 1.71 - 1.83: 237 Bond restraints: 28077 Sorted by residual: bond pdb=" CA GLY A 594 " pdb=" C GLY A 594 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.04e-02 9.25e+03 2.70e+00 bond pdb=" N GLY A 594 " pdb=" CA GLY A 594 " ideal model delta sigma weight residual 1.464 1.447 0.017 1.12e-02 7.97e+03 2.37e+00 bond pdb=" C ALA C 494 " pdb=" N PRO C 495 " ideal model delta sigma weight residual 1.326 1.344 -0.018 1.44e-02 4.82e+03 1.51e+00 bond pdb=" C SER B 897 " pdb=" N PRO B 898 " ideal model delta sigma weight residual 1.335 1.350 -0.016 1.28e-02 6.10e+03 1.47e+00 bond pdb=" N PRO B 93 " pdb=" CA PRO B 93 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.31e-02 5.83e+03 1.38e+00 ... (remaining 28072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 37219 1.39 - 2.78: 822 2.78 - 4.16: 175 4.16 - 5.55: 10 5.55 - 6.94: 6 Bond angle restraints: 38232 Sorted by residual: angle pdb=" N SER C 897 " pdb=" CA SER C 897 " pdb=" C SER C 897 " ideal model delta sigma weight residual 109.81 116.28 -6.47 2.21e+00 2.05e-01 8.57e+00 angle pdb=" N ILE B 394 " pdb=" CA ILE B 394 " pdb=" C ILE B 394 " ideal model delta sigma weight residual 111.91 109.35 2.56 8.90e-01 1.26e+00 8.25e+00 angle pdb=" CA SER C 897 " pdb=" C SER C 897 " pdb=" N PRO C 898 " ideal model delta sigma weight residual 118.44 122.99 -4.55 1.59e+00 3.96e-01 8.21e+00 angle pdb=" N GLY B 563 " pdb=" CA GLY B 563 " pdb=" C GLY B 563 " ideal model delta sigma weight residual 111.37 114.92 -3.55 1.29e+00 6.01e-01 7.56e+00 angle pdb=" C ASP B 892 " pdb=" N ASP B 893 " pdb=" CA ASP B 893 " ideal model delta sigma weight residual 122.40 126.20 -3.80 1.45e+00 4.76e-01 6.86e+00 ... (remaining 38227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 15876 16.89 - 33.78: 700 33.78 - 50.67: 118 50.67 - 67.56: 29 67.56 - 84.45: 11 Dihedral angle restraints: 16734 sinusoidal: 6429 harmonic: 10305 Sorted by residual: dihedral pdb=" CB CYS B 491 " pdb=" SG CYS B 491 " pdb=" SG CYS B 561 " pdb=" CB CYS B 561 " ideal model delta sinusoidal sigma weight residual -86.00 -122.02 36.02 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CB CYS A 491 " pdb=" SG CYS A 491 " pdb=" SG CYS A 561 " pdb=" CB CYS A 561 " ideal model delta sinusoidal sigma weight residual -86.00 -121.59 35.59 1 1.00e+01 1.00e-02 1.79e+01 dihedral pdb=" CB CYS C 491 " pdb=" SG CYS C 491 " pdb=" SG CYS C 561 " pdb=" CB CYS C 561 " ideal model delta sinusoidal sigma weight residual -86.00 -121.40 35.40 1 1.00e+01 1.00e-02 1.78e+01 ... (remaining 16731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2452 0.029 - 0.058: 1088 0.058 - 0.087: 408 0.087 - 0.117: 274 0.117 - 0.146: 98 Chirality restraints: 4320 Sorted by residual: chirality pdb=" CA SER B 897 " pdb=" N SER B 897 " pdb=" C SER B 897 " pdb=" CB SER B 897 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA SER C 897 " pdb=" N SER C 897 " pdb=" C SER C 897 " pdb=" CB SER C 897 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA SER A 897 " pdb=" N SER A 897 " pdb=" C SER A 897 " pdb=" CB SER A 897 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 4317 not shown) Planarity restraints: 4938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 897 " -0.046 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO A 898 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 898 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 898 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 897 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO C 898 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 898 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 898 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 897 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO B 898 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 898 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 898 " -0.038 5.00e-02 4.00e+02 ... (remaining 4935 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 7715 2.82 - 3.34: 20462 3.34 - 3.86: 42769 3.86 - 4.38: 50465 4.38 - 4.90: 90240 Nonbonded interactions: 211651 Sorted by model distance: nonbonded pdb=" OD1 ASN A 895 " pdb=" OG SER A 897 " model vdw 2.294 3.040 nonbonded pdb=" OD1 ASN C 895 " pdb=" OG SER C 897 " model vdw 2.299 3.040 nonbonded pdb=" OD1 ASN B 895 " pdb=" OG SER B 897 " model vdw 2.312 3.040 nonbonded pdb=" OG SER B 37 " pdb=" O ASP B 39 " model vdw 2.314 3.040 nonbonded pdb=" OG SER A 37 " pdb=" O ASP A 39 " model vdw 2.315 3.040 ... (remaining 211646 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 3.460 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 27.540 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.003 0.052 28140 Z= 0.153 Angle : 0.543 6.941 38358 Z= 0.315 Chirality : 0.046 0.146 4320 Planarity : 0.006 0.069 4938 Dihedral : 10.210 84.449 9957 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.76 % Allowed : 3.95 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.13), residues: 3489 helix: -0.68 (0.18), residues: 720 sheet: 0.43 (0.19), residues: 741 loop : -1.28 (0.12), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 413 TYR 0.016 0.002 TYR B 633 PHE 0.020 0.002 PHE B 122 TRP 0.010 0.001 TRP B 460 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (28077) covalent geometry : angle 0.54079 / 0.31 (38232) SS BOND : bond 0.00263 / 0.17 ( 63) SS BOND : angle 0.97944 / 0.66 ( 126) hydrogen bonds : bond 0.24666 / 16.62 ( 1032) hydrogen bonds : angle 7.65589 / 5.27 ( 2931) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 431 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.6964 (m-30) cc_final: 0.6636 (p0) REVERT: A 136 TYR cc_start: 0.8772 (m-80) cc_final: 0.8494 (m-80) REVERT: A 219 GLU cc_start: 0.8348 (tt0) cc_final: 0.8014 (tm-30) REVERT: A 252 MET cc_start: 0.8221 (mtt) cc_final: 0.7864 (mtm) REVERT: A 352 LYS cc_start: 0.8602 (ptpt) cc_final: 0.8333 (ttpp) REVERT: A 463 ARG cc_start: 0.8170 (ttt180) cc_final: 0.7916 (ttm170) REVERT: A 522 CYS cc_start: 0.7076 (m) cc_final: 0.6817 (m) REVERT: A 569 ASP cc_start: 0.7547 (m-30) cc_final: 0.7324 (t0) REVERT: A 746 GLN cc_start: 0.7954 (mt0) cc_final: 0.7540 (tt0) REVERT: A 789 ASP cc_start: 0.8234 (m-30) cc_final: 0.7982 (m-30) REVERT: A 1015 LYS cc_start: 0.6924 (mmtt) cc_final: 0.6653 (mptt) REVERT: A 1165 LYS cc_start: 0.7487 (mttt) cc_final: 0.7009 (mtpm) REVERT: A 1181 ARG cc_start: 0.6255 (mtm180) cc_final: 0.5979 (mtm-85) REVERT: A 1193 VAL cc_start: 0.7376 (t) cc_final: 0.6931 (m) REVERT: A 1232 MET cc_start: 0.6440 (mmt) cc_final: 0.4842 (pmm) REVERT: B 18 ASP cc_start: 0.7109 (m-30) cc_final: 0.6894 (p0) REVERT: B 36 ILE cc_start: 0.8199 (mt) cc_final: 0.7909 (mm) REVERT: B 196 SER cc_start: 0.7826 (m) cc_final: 0.7623 (p) REVERT: B 219 GLU cc_start: 0.8222 (tt0) cc_final: 0.7800 (tm-30) REVERT: B 444 ASN cc_start: 0.8075 (m-40) cc_final: 0.7748 (p0) REVERT: B 463 ARG cc_start: 0.8238 (ttt180) cc_final: 0.7941 (ttp80) REVERT: B 522 CYS cc_start: 0.7086 (m) cc_final: 0.6746 (m) REVERT: B 538 ASP cc_start: 0.7317 (p0) cc_final: 0.6914 (p0) REVERT: B 541 THR cc_start: 0.6705 (m) cc_final: 0.6115 (p) REVERT: B 589 ASP cc_start: 0.8126 (m-30) cc_final: 0.7455 (t0) REVERT: B 610 SER cc_start: 0.8529 (t) cc_final: 0.8085 (m) REVERT: B 698 GLU cc_start: 0.8073 (pt0) cc_final: 0.7596 (pt0) REVERT: B 746 GLN cc_start: 0.7774 (mt0) cc_final: 0.7493 (tt0) REVERT: B 788 ASN cc_start: 0.6903 (m-40) cc_final: 0.6328 (p0) REVERT: B 884 LYS cc_start: 0.7934 (mttt) cc_final: 0.7590 (mttp) REVERT: B 889 PHE cc_start: 0.6820 (p90) cc_final: 0.5888 (m-10) REVERT: B 966 ASN cc_start: 0.8107 (m-40) cc_final: 0.7645 (m-40) REVERT: B 997 GLN cc_start: 0.8242 (mt0) cc_final: 0.8006 (mt0) REVERT: B 1104 GLN cc_start: 0.7327 (mt0) cc_final: 0.7087 (mp10) REVERT: B 1165 LYS cc_start: 0.7583 (mttt) cc_final: 0.7185 (ttmt) REVERT: B 1232 MET cc_start: 0.6258 (mmt) cc_final: 0.4265 (pmm) REVERT: C 18 ASP cc_start: 0.7092 (m-30) cc_final: 0.6518 (p0) REVERT: C 160 GLU cc_start: 0.8013 (tt0) cc_final: 0.7726 (tt0) REVERT: C 244 MET cc_start: 0.7004 (pp-130) cc_final: 0.6760 (mmt) REVERT: C 463 ARG cc_start: 0.8154 (ttt180) cc_final: 0.7889 (ttt-90) REVERT: C 467 ILE cc_start: 0.7732 (mt) cc_final: 0.7491 (mm) REVERT: C 538 ASP cc_start: 0.7253 (p0) cc_final: 0.6963 (p0) REVERT: C 541 THR cc_start: 0.7019 (m) cc_final: 0.6446 (p) REVERT: C 569 ASP cc_start: 0.7851 (m-30) cc_final: 0.7559 (t0) REVERT: C 698 GLU cc_start: 0.7892 (pt0) cc_final: 0.7544 (pt0) REVERT: C 746 GLN cc_start: 0.7900 (mt0) cc_final: 0.7450 (tt0) REVERT: C 789 ASP cc_start: 0.8442 (m-30) cc_final: 0.8209 (m-30) REVERT: C 842 VAL cc_start: 0.8739 (t) cc_final: 0.8533 (m) REVERT: C 889 PHE cc_start: 0.6479 (p90) cc_final: 0.5779 (m-10) REVERT: C 925 LYS cc_start: 0.8307 (tttt) cc_final: 0.7953 (tttp) REVERT: C 1015 LYS cc_start: 0.7122 (mmtt) cc_final: 0.6849 (mppt) REVERT: C 1165 LYS cc_start: 0.7441 (mttt) cc_final: 0.7156 (mtpm) REVERT: C 1170 ARG cc_start: 0.7548 (mtp180) cc_final: 0.7324 (mtp180) REVERT: C 1181 ARG cc_start: 0.6451 (mtm180) cc_final: 0.6055 (mtm180) REVERT: C 1224 ASN cc_start: 0.5619 (OUTLIER) cc_final: 0.4726 (p0) REVERT: C 1232 MET cc_start: 0.6296 (mmt) cc_final: 0.4650 (pmm) outliers start: 54 outliers final: 16 residues processed: 467 average time/residue: 0.4676 time to fit residues: 267.7165 Evaluate side-chains 312 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 295 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 1224 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN A 141 GLN A 156 GLN A 182 ASN A 593 GLN A 695 ASN A1054 ASN B 182 ASN B 593 GLN B 695 ASN B1001 ASN B1139 ASN C 141 GLN C 380 GLN C 444 ASN C 593 GLN C 695 ASN C1054 ASN C1194 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.145222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.112565 restraints weight = 31194.495| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.84 r_work: 0.3041 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28140 Z= 0.121 Angle : 0.496 9.165 38358 Z= 0.279 Chirality : 0.043 0.166 4320 Planarity : 0.005 0.055 4938 Dihedral : 4.827 55.155 3842 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.19 % Allowed : 7.96 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3489 helix: 0.64 (0.20), residues: 741 sheet: 0.29 (0.18), residues: 741 loop : -1.13 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 413 TYR 0.018 0.001 TYR B 443 PHE 0.012 0.001 PHE B 776 TRP 0.011 0.001 TRP C 188 HIS 0.005 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (28077) covalent geometry : angle 0.49180 / 0.28 (38232) SS BOND : bond 0.00241 / 0.16 ( 63) SS BOND : angle 1.23090 / 0.92 ( 126) hydrogen bonds : bond 0.06413 / 4.29 ( 1032) hydrogen bonds : angle 5.55850 / 3.83 ( 2931) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 321 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.6978 (m-30) cc_final: 0.6601 (p0) REVERT: A 81 LYS cc_start: 0.7902 (tttm) cc_final: 0.7510 (ttmm) REVERT: A 136 TYR cc_start: 0.8765 (m-80) cc_final: 0.8480 (m-80) REVERT: A 219 GLU cc_start: 0.8274 (tt0) cc_final: 0.7981 (tm-30) REVERT: A 352 LYS cc_start: 0.8607 (ptpt) cc_final: 0.8329 (ttpp) REVERT: A 463 ARG cc_start: 0.8198 (ttt180) cc_final: 0.7965 (ttm170) REVERT: A 569 ASP cc_start: 0.7575 (m-30) cc_final: 0.7373 (t0) REVERT: A 746 GLN cc_start: 0.7970 (mt0) cc_final: 0.7527 (tt0) REVERT: A 775 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7697 (ptm-80) REVERT: A 789 ASP cc_start: 0.8188 (m-30) cc_final: 0.7984 (m-30) REVERT: A 1015 LYS cc_start: 0.7081 (mmtt) cc_final: 0.6741 (mptt) REVERT: A 1104 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.6123 (mt0) REVERT: A 1165 LYS cc_start: 0.7549 (mttt) cc_final: 0.7041 (mtpm) REVERT: A 1167 VAL cc_start: 0.8093 (p) cc_final: 0.7858 (m) REVERT: A 1232 MET cc_start: 0.6446 (mmt) cc_final: 0.4834 (pmm) REVERT: B 18 ASP cc_start: 0.7102 (m-30) cc_final: 0.6846 (p0) REVERT: B 219 GLU cc_start: 0.7921 (tt0) cc_final: 0.7570 (tm-30) REVERT: B 382 ASP cc_start: 0.8326 (m-30) cc_final: 0.8084 (m-30) REVERT: B 463 ARG cc_start: 0.8156 (ttt180) cc_final: 0.7853 (ttp80) REVERT: B 538 ASP cc_start: 0.7312 (p0) cc_final: 0.6904 (p0) REVERT: B 541 THR cc_start: 0.6603 (m) cc_final: 0.6003 (p) REVERT: B 698 GLU cc_start: 0.8005 (pt0) cc_final: 0.7518 (pt0) REVERT: B 720 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7604 (mp10) REVERT: B 746 GLN cc_start: 0.7843 (mt0) cc_final: 0.7496 (tt0) REVERT: B 775 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7067 (ptm-80) REVERT: B 788 ASN cc_start: 0.6885 (m-40) cc_final: 0.6179 (p0) REVERT: B 799 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7452 (mt-10) REVERT: B 884 LYS cc_start: 0.7890 (mttt) cc_final: 0.7580 (mttp) REVERT: B 889 PHE cc_start: 0.6894 (p90) cc_final: 0.5872 (m-10) REVERT: B 891 VAL cc_start: 0.7317 (p) cc_final: 0.7069 (m) REVERT: B 966 ASN cc_start: 0.8095 (m-40) cc_final: 0.7682 (m-40) REVERT: B 1165 LYS cc_start: 0.7541 (mttt) cc_final: 0.7189 (ttmt) REVERT: B 1224 ASN cc_start: 0.5397 (OUTLIER) cc_final: 0.4853 (p0) REVERT: B 1232 MET cc_start: 0.6254 (mmt) cc_final: 0.4249 (pmm) REVERT: C 18 ASP cc_start: 0.7127 (m-30) cc_final: 0.6530 (p0) REVERT: C 160 GLU cc_start: 0.7708 (tt0) cc_final: 0.7403 (tt0) REVERT: C 444 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7754 (p0) REVERT: C 463 ARG cc_start: 0.8094 (ttt180) cc_final: 0.7805 (ttt-90) REVERT: C 538 ASP cc_start: 0.7207 (p0) cc_final: 0.6843 (p0) REVERT: C 541 THR cc_start: 0.6971 (m) cc_final: 0.6415 (p) REVERT: C 698 GLU cc_start: 0.7815 (pt0) cc_final: 0.7467 (pt0) REVERT: C 720 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7564 (mp10) REVERT: C 746 GLN cc_start: 0.7941 (mt0) cc_final: 0.7424 (tt0) REVERT: C 775 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7077 (ptm-80) REVERT: C 889 PHE cc_start: 0.6334 (p90) cc_final: 0.5704 (m-10) REVERT: C 925 LYS cc_start: 0.8329 (tttt) cc_final: 0.7949 (tttp) REVERT: C 1015 LYS cc_start: 0.7295 (mmtt) cc_final: 0.6649 (mmpt) REVERT: C 1165 LYS cc_start: 0.7348 (mttt) cc_final: 0.7006 (mtpm) REVERT: C 1170 ARG cc_start: 0.7724 (mtp180) cc_final: 0.7373 (mtp180) REVERT: C 1181 ARG cc_start: 0.5998 (mtm180) cc_final: 0.5660 (mtm180) REVERT: C 1198 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7324 (mtp) REVERT: C 1224 ASN cc_start: 0.5636 (OUTLIER) cc_final: 0.4702 (p0) REVERT: C 1232 MET cc_start: 0.6306 (mmt) cc_final: 0.4649 (pmm) outliers start: 67 outliers final: 31 residues processed: 361 average time/residue: 0.4948 time to fit residues: 216.8903 Evaluate side-chains 333 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 292 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 1104 GLN Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 944 ILE Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 720 GLN Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 759 ASP Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1198 MET Chi-restraints excluded: chain C residue 1224 ASN Chi-restraints excluded: chain C residue 1226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [140, 248, 190, 93, 13, 286, 169, 182, 150, 133, 191] chunk 140 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 286 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 133 optimal weight: 0.0770 chunk 191 optimal weight: 2.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN A 156 GLN A 593 GLN B 141 GLN B 593 GLN B 709 ASN B1104 GLN B1139 ASN C 27 ASN C 444 ASN C 593 GLN C1194 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.143339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109869 restraints weight = 31130.767| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.80 r_work: 0.3015 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28140 Z= 0.147 Angle : 0.519 9.622 38358 Z= 0.288 Chirality : 0.044 0.148 4320 Planarity : 0.005 0.055 4938 Dihedral : 4.725 55.364 3836 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.54 % Allowed : 8.58 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3489 helix: 1.01 (0.20), residues: 741 sheet: 0.40 (0.18), residues: 738 loop : -1.16 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1133 TYR 0.017 0.002 TYR A 633 PHE 0.014 0.001 PHE B 776 TRP 0.011 0.001 TRP A 348 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (28077) covalent geometry : angle 0.51381 / 0.29 (38232) SS BOND : bond 0.00333 / 0.22 ( 63) SS BOND : angle 1.38139 / 1.06 ( 126) hydrogen bonds : bond 0.06549 / 4.39 ( 1032) hydrogen bonds : angle 5.27472 / 3.64 ( 2931) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 281 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7019 (m-30) cc_final: 0.6679 (p0) REVERT: A 81 LYS cc_start: 0.8137 (tttm) cc_final: 0.7740 (ttmm) REVERT: A 136 TYR cc_start: 0.8777 (m-80) cc_final: 0.8528 (m-80) REVERT: A 168 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7625 (mmm) REVERT: A 219 GLU cc_start: 0.8314 (tt0) cc_final: 0.8001 (tm-30) REVERT: A 352 LYS cc_start: 0.8715 (ptpt) cc_final: 0.8451 (ttpp) REVERT: A 463 ARG cc_start: 0.8280 (ttt180) cc_final: 0.8034 (ttm170) REVERT: A 720 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: A 746 GLN cc_start: 0.7937 (mt0) cc_final: 0.7599 (tt0) REVERT: A 775 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7849 (ptm-80) REVERT: A 789 ASP cc_start: 0.8219 (m-30) cc_final: 0.8018 (m-30) REVERT: A 1015 LYS cc_start: 0.7195 (mmtt) cc_final: 0.6844 (mptt) REVERT: A 1104 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.6226 (mt0) REVERT: A 1165 LYS cc_start: 0.7701 (mttt) cc_final: 0.7207 (mtpm) REVERT: A 1167 VAL cc_start: 0.8121 (p) cc_final: 0.7881 (m) REVERT: A 1198 MET cc_start: 0.7948 (mtt) cc_final: 0.7540 (mtt) REVERT: A 1218 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6750 (mtm) REVERT: A 1232 MET cc_start: 0.6368 (mmt) cc_final: 0.4839 (pmm) REVERT: B 64 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8580 (mt) REVERT: B 219 GLU cc_start: 0.7930 (tt0) cc_final: 0.7574 (tm-30) REVERT: B 463 ARG cc_start: 0.8243 (ttt180) cc_final: 0.7915 (ttp80) REVERT: B 698 GLU cc_start: 0.8118 (pt0) cc_final: 0.7619 (pt0) REVERT: B 746 GLN cc_start: 0.7892 (mt0) cc_final: 0.7570 (tt0) REVERT: B 775 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7205 (ptm-80) REVERT: B 788 ASN cc_start: 0.6909 (m-40) cc_final: 0.6278 (p0) REVERT: B 799 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7640 (mt-10) REVERT: B 884 LYS cc_start: 0.7912 (mttt) cc_final: 0.7591 (mttp) REVERT: B 889 PHE cc_start: 0.6969 (p90) cc_final: 0.5987 (m-10) REVERT: B 966 ASN cc_start: 0.8138 (m-40) cc_final: 0.7735 (m-40) REVERT: B 1165 LYS cc_start: 0.7639 (mttt) cc_final: 0.7321 (ttmt) REVERT: B 1224 ASN cc_start: 0.5430 (OUTLIER) cc_final: 0.4890 (p0) REVERT: B 1232 MET cc_start: 0.6262 (mmt) cc_final: 0.4281 (pmm) REVERT: C 18 ASP cc_start: 0.7239 (m-30) cc_final: 0.6621 (p0) REVERT: C 160 GLU cc_start: 0.7614 (tt0) cc_final: 0.7312 (tt0) REVERT: C 168 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7523 (mmm) REVERT: C 462 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7418 (mptt) REVERT: C 463 ARG cc_start: 0.8154 (ttt180) cc_final: 0.7822 (ttt-90) REVERT: C 538 ASP cc_start: 0.7333 (p0) cc_final: 0.6978 (p0) REVERT: C 541 THR cc_start: 0.7036 (m) cc_final: 0.6519 (p) REVERT: C 698 GLU cc_start: 0.7928 (pt0) cc_final: 0.7665 (pt0) REVERT: C 720 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: C 746 GLN cc_start: 0.7972 (mt0) cc_final: 0.7498 (tt0) REVERT: C 775 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7187 (ptm-80) REVERT: C 889 PHE cc_start: 0.6549 (p90) cc_final: 0.5842 (m-10) REVERT: C 1015 LYS cc_start: 0.7350 (mmtt) cc_final: 0.6663 (mmpt) REVERT: C 1104 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.6857 (mt0) REVERT: C 1165 LYS cc_start: 0.7494 (mttt) cc_final: 0.7150 (mtpm) REVERT: C 1170 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7590 (mtp-110) REVERT: C 1181 ARG cc_start: 0.6163 (mtm180) cc_final: 0.5728 (mtm180) REVERT: C 1224 ASN cc_start: 0.5619 (OUTLIER) cc_final: 0.4676 (p0) REVERT: C 1232 MET cc_start: 0.6298 (mmt) cc_final: 0.4728 (pmm) outliers start: 78 outliers final: 41 residues processed: 330 average time/residue: 0.5128 time to fit residues: 204.7126 Evaluate side-chains 324 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 269 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 720 GLN Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 1104 GLN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1218 MET Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 944 ILE Chi-restraints excluded: chain B residue 1104 GLN Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 568 SER Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 720 GLN Chi-restraints excluded: chain C residue 759 ASP Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 1104 GLN Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1224 ASN Chi-restraints excluded: chain C residue 1226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [52, 183, 115, 234, 344, 268, 132, 69, 27, 118, 199] chunk 52 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 234 optimal weight: 8.9990 chunk 344 optimal weight: 3.9990 chunk 268 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 199 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN A 141 GLN A 593 GLN B 593 GLN B1139 ASN C 27 ASN C 593 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.144002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.109663 restraints weight = 31262.965| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.97 r_work: 0.2966 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28140 Z= 0.207 Angle : 0.595 9.064 38358 Z= 0.326 Chirality : 0.047 0.151 4320 Planarity : 0.005 0.052 4938 Dihedral : 4.884 44.381 3832 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.16 % Allowed : 8.77 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3489 helix: 0.96 (0.20), residues: 741 sheet: 0.33 (0.18), residues: 762 loop : -1.28 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1133 TYR 0.022 0.002 TYR C 844 PHE 0.017 0.002 PHE C1114 TRP 0.013 0.002 TRP A 348 HIS 0.007 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 (28077) covalent geometry : angle 0.58833 / 0.32 (38232) SS BOND : bond 0.00439 / 0.28 ( 63) SS BOND : angle 1.60404 / 1.21 ( 126) hydrogen bonds : bond 0.07582 / 5.10 ( 1032) hydrogen bonds : angle 5.32387 / 3.66 ( 2931) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 266 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.8224 (tttm) cc_final: 0.7878 (ttmm) REVERT: A 168 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7987 (mmm) REVERT: A 219 GLU cc_start: 0.8522 (tt0) cc_final: 0.8318 (tm-30) REVERT: A 344 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8318 (t0) REVERT: A 352 LYS cc_start: 0.9007 (ptpt) cc_final: 0.8791 (ttpp) REVERT: A 463 ARG cc_start: 0.8578 (ttt180) cc_final: 0.8299 (ttm170) REVERT: A 720 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: A 746 GLN cc_start: 0.8212 (mt0) cc_final: 0.7946 (tt0) REVERT: A 775 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8321 (ptm-80) REVERT: A 833 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8140 (t0) REVERT: A 1015 LYS cc_start: 0.7586 (mmtt) cc_final: 0.7206 (mptt) REVERT: A 1104 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.6899 (mt0) REVERT: A 1165 LYS cc_start: 0.8166 (mttt) cc_final: 0.7747 (mtpm) REVERT: A 1198 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7847 (mtt) REVERT: A 1218 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6778 (mtt) REVERT: A 1232 MET cc_start: 0.6462 (mmt) cc_final: 0.4850 (pmm) REVERT: B 463 ARG cc_start: 0.8562 (ttt180) cc_final: 0.8312 (ttp80) REVERT: B 522 CYS cc_start: 0.7007 (m) cc_final: 0.6604 (m) REVERT: B 541 THR cc_start: 0.7051 (m) cc_final: 0.6644 (p) REVERT: B 624 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8465 (m-30) REVERT: B 698 GLU cc_start: 0.8496 (pt0) cc_final: 0.8105 (pt0) REVERT: B 720 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: B 746 GLN cc_start: 0.8166 (mt0) cc_final: 0.7922 (tt0) REVERT: B 775 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7653 (ptm-80) REVERT: B 799 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7867 (mt-10) REVERT: B 884 LYS cc_start: 0.8090 (mttt) cc_final: 0.7784 (mttp) REVERT: B 885 ASP cc_start: 0.5688 (m-30) cc_final: 0.5424 (m-30) REVERT: B 966 ASN cc_start: 0.8506 (m-40) cc_final: 0.8142 (m-40) REVERT: B 1165 LYS cc_start: 0.8113 (mttt) cc_final: 0.7837 (ttmt) REVERT: B 1218 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6879 (mtm) REVERT: B 1224 ASN cc_start: 0.5464 (OUTLIER) cc_final: 0.4892 (p0) REVERT: B 1232 MET cc_start: 0.6343 (mmt) cc_final: 0.4359 (pmm) REVERT: C 168 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7893 (mmm) REVERT: C 352 LYS cc_start: 0.9054 (ptpt) cc_final: 0.8823 (ttpp) REVERT: C 462 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7987 (mptt) REVERT: C 463 ARG cc_start: 0.8417 (ttt180) cc_final: 0.8128 (ttt180) REVERT: C 538 ASP cc_start: 0.7688 (p0) cc_final: 0.7306 (p0) REVERT: C 541 THR cc_start: 0.7318 (m) cc_final: 0.6776 (p) REVERT: C 648 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8149 (m-40) REVERT: C 698 GLU cc_start: 0.8395 (pt0) cc_final: 0.8147 (pt0) REVERT: C 720 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: C 746 GLN cc_start: 0.8277 (mt0) cc_final: 0.7888 (tt0) REVERT: C 775 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7721 (ptm-80) REVERT: C 889 PHE cc_start: 0.7050 (p90) cc_final: 0.6451 (m-10) REVERT: C 1015 LYS cc_start: 0.7616 (mmtt) cc_final: 0.6981 (mmpt) REVERT: C 1104 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.6981 (mt0) REVERT: C 1165 LYS cc_start: 0.7981 (mttt) cc_final: 0.7705 (mtpm) REVERT: C 1181 ARG cc_start: 0.6609 (mtm180) cc_final: 0.6181 (mtm180) REVERT: C 1224 ASN cc_start: 0.5661 (OUTLIER) cc_final: 0.4758 (p0) REVERT: C 1232 MET cc_start: 0.6414 (mmt) cc_final: 0.4791 (pmm) outliers start: 97 outliers final: 49 residues processed: 332 average time/residue: 0.5039 time to fit residues: 203.0546 Evaluate side-chains 329 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 260 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 720 GLN Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1104 GLN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1218 MET Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 872 SER Chi-restraints excluded: chain B residue 944 ILE Chi-restraints excluded: chain B residue 1180 ASP Chi-restraints excluded: chain B residue 1200 THR Chi-restraints excluded: chain B residue 1218 MET Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 568 SER Chi-restraints excluded: chain C residue 648 ASN Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 720 GLN Chi-restraints excluded: chain C residue 759 ASP Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 1104 GLN Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1224 ASN Chi-restraints excluded: chain C residue 1226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [328, 214, 47, 279, 282, 81, 345, 250, 45, 219, 259] chunk 328 optimal weight: 3.9990 chunk 214 optimal weight: 0.4980 chunk 47 optimal weight: 10.0000 chunk 279 optimal weight: 0.8980 chunk 282 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 345 optimal weight: 1.9990 chunk 250 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 259 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN A 593 GLN B 593 GLN B 695 ASN B1139 ASN C 27 ASN C 593 GLN C 695 ASN C1194 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.143211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.110578 restraints weight = 30952.774| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.73 r_work: 0.3029 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28140 Z= 0.115 Angle : 0.479 9.262 38358 Z= 0.268 Chirality : 0.043 0.142 4320 Planarity : 0.004 0.051 4938 Dihedral : 4.484 42.782 3829 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.45 % Allowed : 9.98 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.14), residues: 3489 helix: 1.37 (0.20), residues: 738 sheet: 0.46 (0.18), residues: 732 loop : -1.17 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 945 TYR 0.014 0.001 TYR B 443 PHE 0.012 0.001 PHE B 776 TRP 0.012 0.001 TRP C 188 HIS 0.004 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (28077) covalent geometry : angle 0.47568 / 0.27 (38232) SS BOND : bond 0.00259 / 0.16 ( 63) SS BOND : angle 1.11902 / 0.84 ( 126) hydrogen bonds : bond 0.06020 / 4.04 ( 1032) hydrogen bonds : angle 5.04471 / 3.47 ( 2931) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 277 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.8115 (tttm) cc_final: 0.7690 (ttmm) REVERT: A 168 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7626 (mmm) REVERT: A 219 GLU cc_start: 0.8285 (tt0) cc_final: 0.7917 (tm-30) REVERT: A 344 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7809 (t0) REVERT: A 352 LYS cc_start: 0.8731 (ptpt) cc_final: 0.8473 (ttpp) REVERT: A 463 ARG cc_start: 0.8269 (ttt180) cc_final: 0.7972 (ttm170) REVERT: A 720 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7611 (mp10) REVERT: A 746 GLN cc_start: 0.7893 (mt0) cc_final: 0.7534 (tt0) REVERT: A 759 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7212 (t70) REVERT: A 775 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7660 (ptm-80) REVERT: A 833 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7728 (t0) REVERT: A 925 LYS cc_start: 0.8102 (tttp) cc_final: 0.7875 (tttm) REVERT: A 1015 LYS cc_start: 0.7162 (mmtt) cc_final: 0.6768 (mptt) REVERT: A 1165 LYS cc_start: 0.7709 (mttt) cc_final: 0.7172 (mtpm) REVERT: A 1167 VAL cc_start: 0.8097 (p) cc_final: 0.7877 (m) REVERT: A 1198 MET cc_start: 0.7897 (mtt) cc_final: 0.7415 (mtt) REVERT: A 1232 MET cc_start: 0.6421 (mmt) cc_final: 0.4861 (pmm) REVERT: B 120 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8468 (p) REVERT: B 463 ARG cc_start: 0.8213 (ttt180) cc_final: 0.7958 (ttp80) REVERT: B 522 CYS cc_start: 0.6833 (m) cc_final: 0.6425 (m) REVERT: B 698 GLU cc_start: 0.8077 (pt0) cc_final: 0.7561 (pt0) REVERT: B 720 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7601 (mp10) REVERT: B 746 GLN cc_start: 0.7817 (mt0) cc_final: 0.7501 (tt0) REVERT: B 775 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7491 (mtm180) REVERT: B 799 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7694 (mt-10) REVERT: B 884 LYS cc_start: 0.7932 (mttt) cc_final: 0.7607 (mttp) REVERT: B 885 ASP cc_start: 0.5472 (m-30) cc_final: 0.5171 (m-30) REVERT: B 966 ASN cc_start: 0.8045 (m-40) cc_final: 0.7670 (m-40) REVERT: B 1165 LYS cc_start: 0.7711 (mttt) cc_final: 0.7337 (ttmt) REVERT: B 1224 ASN cc_start: 0.5306 (OUTLIER) cc_final: 0.4768 (p0) REVERT: B 1232 MET cc_start: 0.6310 (mmt) cc_final: 0.4403 (pmm) REVERT: C 168 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7541 (mmm) REVERT: C 463 ARG cc_start: 0.8085 (ttt180) cc_final: 0.7824 (ttt180) REVERT: C 538 ASP cc_start: 0.7408 (p0) cc_final: 0.7076 (p0) REVERT: C 541 THR cc_start: 0.6948 (m) cc_final: 0.6436 (p) REVERT: C 698 GLU cc_start: 0.7967 (pt0) cc_final: 0.7669 (pt0) REVERT: C 720 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: C 746 GLN cc_start: 0.7939 (mt0) cc_final: 0.7450 (tt0) REVERT: C 775 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7237 (ptm-80) REVERT: C 889 PHE cc_start: 0.6508 (p90) cc_final: 0.5829 (m-10) REVERT: C 1015 LYS cc_start: 0.7226 (mmtt) cc_final: 0.6552 (mmpt) REVERT: C 1104 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.6869 (mt0) REVERT: C 1165 LYS cc_start: 0.7505 (mttt) cc_final: 0.7108 (mtpm) REVERT: C 1181 ARG cc_start: 0.6075 (mtm180) cc_final: 0.5750 (mtm180) REVERT: C 1224 ASN cc_start: 0.5626 (OUTLIER) cc_final: 0.4591 (p0) REVERT: C 1232 MET cc_start: 0.6336 (mmt) cc_final: 0.4763 (pmm) outliers start: 75 outliers final: 38 residues processed: 323 average time/residue: 0.5153 time to fit residues: 201.1663 Evaluate side-chains 320 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 267 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 720 GLN Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1180 ASP Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 720 GLN Chi-restraints excluded: chain C residue 759 ASP Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 1104 GLN Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1180 ASP Chi-restraints excluded: chain C residue 1224 ASN Chi-restraints excluded: chain C residue 1226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [156, 101, 263, 212, 68, 307, 280, 29, 82, 294, 241] chunk 156 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 307 optimal weight: 10.0000 chunk 280 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 294 optimal weight: 6.9990 chunk 241 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN A 593 GLN B 27 ASN B 593 GLN B 695 ASN B1139 ASN C 27 ASN C 141 GLN C 593 GLN C 695 ASN C1194 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.144141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.110274 restraints weight = 31165.667| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.89 r_work: 0.2960 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 28140 Z= 0.194 Angle : 0.575 8.161 38358 Z= 0.315 Chirality : 0.047 0.237 4320 Planarity : 0.005 0.053 4938 Dihedral : 4.722 43.689 3827 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.94 % Allowed : 9.82 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3489 helix: 1.18 (0.20), residues: 741 sheet: 0.43 (0.18), residues: 753 loop : -1.27 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1133 TYR 0.020 0.002 TYR B 633 PHE 0.016 0.002 PHE A 122 TRP 0.014 0.002 TRP A 348 HIS 0.007 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.19 (28077) covalent geometry : angle 0.57128 / 0.31 (38232) SS BOND : bond 0.00384 / 0.24 ( 63) SS BOND : angle 1.31454 / 0.96 ( 126) hydrogen bonds : bond 0.07329 / 4.91 ( 1032) hydrogen bonds : angle 5.19580 / 3.58 ( 2931) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 264 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8013 (mmm) REVERT: A 219 GLU cc_start: 0.8533 (tt0) cc_final: 0.8312 (tm-30) REVERT: A 344 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8242 (t0) REVERT: A 352 LYS cc_start: 0.9019 (ptpt) cc_final: 0.8793 (ttpp) REVERT: A 463 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8404 (ttt180) REVERT: A 720 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: A 746 GLN cc_start: 0.8223 (mt0) cc_final: 0.7942 (tt0) REVERT: A 775 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8304 (ptm-80) REVERT: A 833 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8206 (t0) REVERT: A 966 ASN cc_start: 0.8488 (m-40) cc_final: 0.8159 (m-40) REVERT: A 1015 LYS cc_start: 0.7603 (mmtt) cc_final: 0.7202 (mptt) REVERT: A 1165 LYS cc_start: 0.8168 (mttt) cc_final: 0.7742 (mtpm) REVERT: A 1198 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7878 (mtt) REVERT: A 1232 MET cc_start: 0.6442 (mmt) cc_final: 0.4848 (pmm) REVERT: B 219 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: B 463 ARG cc_start: 0.8528 (ttt180) cc_final: 0.8229 (ttt180) REVERT: B 517 ASN cc_start: 0.4501 (OUTLIER) cc_final: 0.3815 (t0) REVERT: B 522 CYS cc_start: 0.7034 (m) cc_final: 0.6645 (m) REVERT: B 698 GLU cc_start: 0.8524 (pt0) cc_final: 0.8133 (pt0) REVERT: B 720 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7795 (mp10) REVERT: B 746 GLN cc_start: 0.8191 (mt0) cc_final: 0.7948 (tt0) REVERT: B 775 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7671 (ptm-80) REVERT: B 799 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7945 (mt-10) REVERT: B 884 LYS cc_start: 0.8106 (mttt) cc_final: 0.7795 (mttp) REVERT: B 885 ASP cc_start: 0.5629 (m-30) cc_final: 0.5410 (m-30) REVERT: B 966 ASN cc_start: 0.8509 (m-40) cc_final: 0.8156 (m-40) REVERT: B 1165 LYS cc_start: 0.8148 (mttt) cc_final: 0.7845 (ttmt) REVERT: B 1218 MET cc_start: 0.7213 (mtm) cc_final: 0.6945 (mtm) REVERT: B 1224 ASN cc_start: 0.5594 (OUTLIER) cc_final: 0.5002 (p0) REVERT: B 1232 MET cc_start: 0.6491 (mmt) cc_final: 0.4507 (pmm) REVERT: C 168 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7827 (mmm) REVERT: C 352 LYS cc_start: 0.9040 (ptpt) cc_final: 0.8833 (ttpp) REVERT: C 538 ASP cc_start: 0.7730 (p0) cc_final: 0.7355 (p0) REVERT: C 541 THR cc_start: 0.7246 (m) cc_final: 0.6706 (p) REVERT: C 624 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8386 (t0) REVERT: C 648 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.8129 (m-40) REVERT: C 698 GLU cc_start: 0.8422 (pt0) cc_final: 0.8184 (pt0) REVERT: C 720 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7638 (mp10) REVERT: C 746 GLN cc_start: 0.8308 (mt0) cc_final: 0.7908 (tt0) REVERT: C 775 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7833 (ptm-80) REVERT: C 889 PHE cc_start: 0.6980 (p90) cc_final: 0.6312 (m-10) REVERT: C 1015 LYS cc_start: 0.7603 (mmtt) cc_final: 0.6958 (mmpt) REVERT: C 1104 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.6998 (mt0) REVERT: C 1165 LYS cc_start: 0.7978 (mttt) cc_final: 0.7668 (mtpm) REVERT: C 1224 ASN cc_start: 0.6025 (OUTLIER) cc_final: 0.4945 (p0) REVERT: C 1232 MET cc_start: 0.6418 (mmt) cc_final: 0.5042 (pmm) outliers start: 90 outliers final: 50 residues processed: 325 average time/residue: 0.5087 time to fit residues: 199.9448 Evaluate side-chains 327 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 259 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 720 GLN Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 872 SER Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 548 CYS Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 648 ASN Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 720 GLN Chi-restraints excluded: chain C residue 738 TYR Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 759 ASP Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 1005 VAL Chi-restraints excluded: chain C residue 1104 GLN Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1224 ASN Chi-restraints excluded: chain C residue 1226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [76, 78, 43, 261, 80, 119, 138, 167, 340, 126, 242] chunk 76 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 119 optimal weight: 0.0060 chunk 138 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 340 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN A 593 GLN B 27 ASN B 593 GLN B 695 ASN B1139 ASN C 27 ASN C 593 GLN C 695 ASN C1194 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.147480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113208 restraints weight = 31026.389| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.88 r_work: 0.3030 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 28140 Z= 0.098 Angle : 0.456 5.534 38358 Z= 0.257 Chirality : 0.042 0.140 4320 Planarity : 0.004 0.050 4938 Dihedral : 4.374 41.873 3827 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.22 % Allowed : 10.70 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3489 helix: 1.61 (0.20), residues: 735 sheet: 0.50 (0.18), residues: 732 loop : -1.10 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1133 TYR 0.012 0.001 TYR B 738 PHE 0.013 0.001 PHE A 407 TRP 0.012 0.001 TRP A 460 HIS 0.003 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.10 (28077) covalent geometry : angle 0.45505 / 0.26 (38232) SS BOND : bond 0.00225 / 0.13 ( 63) SS BOND : angle 0.76503 / 0.56 ( 126) hydrogen bonds : bond 0.05664 / 3.80 ( 1032) hydrogen bonds : angle 4.94317 / 3.40 ( 2931) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 270 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7899 (mmm) REVERT: A 219 GLU cc_start: 0.8474 (tt0) cc_final: 0.8207 (tm-30) REVERT: A 344 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8218 (t0) REVERT: A 352 LYS cc_start: 0.8932 (ptpt) cc_final: 0.8723 (ttpp) REVERT: A 463 ARG cc_start: 0.8596 (ttt180) cc_final: 0.8331 (ttt90) REVERT: A 714 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.6963 (m110) REVERT: A 720 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7724 (mp10) REVERT: A 746 GLN cc_start: 0.8171 (mt0) cc_final: 0.7903 (tt0) REVERT: A 775 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8063 (ptm-80) REVERT: A 833 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8061 (t0) REVERT: A 1015 LYS cc_start: 0.7517 (mmtt) cc_final: 0.7146 (mptt) REVERT: A 1165 LYS cc_start: 0.8122 (mttt) cc_final: 0.7709 (mtpm) REVERT: A 1167 VAL cc_start: 0.8456 (p) cc_final: 0.8247 (m) REVERT: A 1198 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7807 (mtt) REVERT: A 1232 MET cc_start: 0.6474 (mmt) cc_final: 0.4905 (pmm) REVERT: B 120 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8619 (p) REVERT: B 219 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: B 463 ARG cc_start: 0.8512 (ttt180) cc_final: 0.8275 (ttp80) REVERT: B 517 ASN cc_start: 0.4260 (OUTLIER) cc_final: 0.3543 (t0) REVERT: B 522 CYS cc_start: 0.7005 (m) cc_final: 0.6650 (m) REVERT: B 610 SER cc_start: 0.8643 (t) cc_final: 0.8396 (m) REVERT: B 698 GLU cc_start: 0.8423 (pt0) cc_final: 0.7980 (pt0) REVERT: B 720 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: B 746 GLN cc_start: 0.8114 (mt0) cc_final: 0.7882 (tt0) REVERT: B 775 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8180 (mtm180) REVERT: B 799 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7884 (mt-10) REVERT: B 884 LYS cc_start: 0.8110 (mttt) cc_final: 0.7804 (mttp) REVERT: B 885 ASP cc_start: 0.5491 (m-30) cc_final: 0.5227 (m-30) REVERT: B 923 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8440 (tppp) REVERT: B 966 ASN cc_start: 0.8393 (m-40) cc_final: 0.8011 (m-40) REVERT: B 1165 LYS cc_start: 0.8062 (mttt) cc_final: 0.7764 (ttmt) REVERT: B 1218 MET cc_start: 0.7207 (mtm) cc_final: 0.6650 (mtt) REVERT: B 1224 ASN cc_start: 0.5755 (OUTLIER) cc_final: 0.5168 (p0) REVERT: B 1232 MET cc_start: 0.6468 (mmt) cc_final: 0.4515 (pmm) REVERT: C 168 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7977 (mmm) REVERT: C 462 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7949 (mptp) REVERT: C 538 ASP cc_start: 0.7703 (p0) cc_final: 0.7335 (p0) REVERT: C 541 THR cc_start: 0.7265 (m) cc_final: 0.6749 (p) REVERT: C 698 GLU cc_start: 0.8255 (pt0) cc_final: 0.8013 (pt0) REVERT: C 720 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: C 746 GLN cc_start: 0.8236 (mt0) cc_final: 0.7856 (tt0) REVERT: C 775 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7511 (ptm-80) REVERT: C 889 PHE cc_start: 0.6922 (p90) cc_final: 0.6284 (m-10) REVERT: C 1015 LYS cc_start: 0.7559 (mmtt) cc_final: 0.7093 (mtpm) REVERT: C 1104 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7377 (mt0) REVERT: C 1165 LYS cc_start: 0.7919 (mttt) cc_final: 0.7627 (mtpm) REVERT: C 1224 ASN cc_start: 0.5941 (OUTLIER) cc_final: 0.4908 (p0) REVERT: C 1232 MET cc_start: 0.6446 (mmt) cc_final: 0.4855 (pmm) outliers start: 68 outliers final: 35 residues processed: 315 average time/residue: 0.5212 time to fit residues: 197.9321 Evaluate side-chains 315 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 261 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 720 GLN Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1180 ASP Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 872 SER Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1180 ASP Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 720 GLN Chi-restraints excluded: chain C residue 759 ASP Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 1104 GLN Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1224 ASN Chi-restraints excluded: chain C residue 1226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [155, 224, 285, 347, 311, 183, 64, 27, 255, 30, 26] chunk 155 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 285 optimal weight: 0.5980 chunk 347 optimal weight: 2.9990 chunk 311 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 64 optimal weight: 0.0060 chunk 27 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN A 156 GLN A 165 GLN A 593 GLN B 593 GLN B 695 ASN B1139 ASN C 27 ASN C 593 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.147621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.113158 restraints weight = 31101.378| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.95 r_work: 0.3026 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 28140 Z= 0.108 Angle : 0.463 6.743 38358 Z= 0.257 Chirality : 0.043 0.141 4320 Planarity : 0.004 0.049 4938 Dihedral : 4.262 40.442 3826 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.32 % Allowed : 10.83 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3489 helix: 1.70 (0.20), residues: 732 sheet: 0.56 (0.18), residues: 750 loop : -1.10 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 999 TYR 0.014 0.001 TYR B 443 PHE 0.012 0.001 PHE B 407 TRP 0.011 0.001 TRP A 460 HIS 0.004 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (28077) covalent geometry : angle 0.46143 / 0.26 (38232) SS BOND : bond 0.00236 / 0.14 ( 63) SS BOND : angle 0.81629 / 0.57 ( 126) hydrogen bonds : bond 0.05649 / 3.79 ( 1032) hydrogen bonds : angle 4.85543 / 3.34 ( 2931) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 262 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7893 (mmm) REVERT: A 219 GLU cc_start: 0.8497 (tt0) cc_final: 0.8241 (tm-30) REVERT: A 344 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8329 (t0) REVERT: A 352 LYS cc_start: 0.8940 (ptpt) cc_final: 0.8723 (ttpp) REVERT: A 463 ARG cc_start: 0.8602 (ttt180) cc_final: 0.8337 (ttt90) REVERT: A 714 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.6978 (m110) REVERT: A 720 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: A 746 GLN cc_start: 0.8192 (mt0) cc_final: 0.7922 (tt0) REVERT: A 775 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8120 (ptm-80) REVERT: A 833 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8070 (t0) REVERT: A 1015 LYS cc_start: 0.7527 (mmtt) cc_final: 0.7143 (mptt) REVERT: A 1165 LYS cc_start: 0.8084 (mttt) cc_final: 0.7675 (mtpm) REVERT: A 1167 VAL cc_start: 0.8458 (p) cc_final: 0.8253 (m) REVERT: A 1198 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7790 (mtt) REVERT: A 1232 MET cc_start: 0.6467 (mmt) cc_final: 0.4893 (pmm) REVERT: B 120 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8620 (p) REVERT: B 201 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6930 (ttt180) REVERT: B 219 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: B 463 ARG cc_start: 0.8488 (ttt180) cc_final: 0.8245 (ttp80) REVERT: B 517 ASN cc_start: 0.4315 (OUTLIER) cc_final: 0.3481 (t0) REVERT: B 522 CYS cc_start: 0.7013 (m) cc_final: 0.6662 (m) REVERT: B 605 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8228 (mt) REVERT: B 698 GLU cc_start: 0.8430 (pt0) cc_final: 0.7991 (pt0) REVERT: B 720 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7695 (mp10) REVERT: B 746 GLN cc_start: 0.8119 (mt0) cc_final: 0.7889 (tt0) REVERT: B 775 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8198 (mtm180) REVERT: B 799 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 884 LYS cc_start: 0.8124 (mttt) cc_final: 0.7820 (mttp) REVERT: B 885 ASP cc_start: 0.5675 (m-30) cc_final: 0.5453 (m-30) REVERT: B 923 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8443 (tppp) REVERT: B 966 ASN cc_start: 0.8414 (m-40) cc_final: 0.8059 (m-40) REVERT: B 1165 LYS cc_start: 0.8104 (mttt) cc_final: 0.7818 (ttmt) REVERT: B 1218 MET cc_start: 0.7221 (mtm) cc_final: 0.6964 (mtm) REVERT: B 1224 ASN cc_start: 0.5776 (OUTLIER) cc_final: 0.5176 (p0) REVERT: B 1232 MET cc_start: 0.6464 (mmt) cc_final: 0.4496 (pmm) REVERT: C 168 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8034 (mmm) REVERT: C 462 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7944 (mptp) REVERT: C 538 ASP cc_start: 0.7671 (p0) cc_final: 0.7285 (p0) REVERT: C 541 THR cc_start: 0.7227 (m) cc_final: 0.6719 (p) REVERT: C 698 GLU cc_start: 0.8248 (pt0) cc_final: 0.8009 (pt0) REVERT: C 720 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7590 (mp10) REVERT: C 746 GLN cc_start: 0.8242 (mt0) cc_final: 0.7863 (tt0) REVERT: C 775 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7736 (ptm-80) REVERT: C 889 PHE cc_start: 0.6958 (p90) cc_final: 0.6311 (m-10) REVERT: C 1015 LYS cc_start: 0.7488 (mmtt) cc_final: 0.6998 (mtpm) REVERT: C 1104 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7367 (mt0) REVERT: C 1165 LYS cc_start: 0.7954 (mttt) cc_final: 0.7655 (mtpm) REVERT: C 1198 MET cc_start: 0.8424 (mtp) cc_final: 0.7734 (mtt) REVERT: C 1224 ASN cc_start: 0.5867 (OUTLIER) cc_final: 0.4952 (p0) REVERT: C 1232 MET cc_start: 0.6435 (mmt) cc_final: 0.4838 (pmm) outliers start: 71 outliers final: 36 residues processed: 309 average time/residue: 0.5191 time to fit residues: 193.8325 Evaluate side-chains 316 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 259 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 720 GLN Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 872 SER Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 720 GLN Chi-restraints excluded: chain C residue 759 ASP Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 1104 GLN Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1224 ASN Chi-restraints excluded: chain C residue 1226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [29, 330, 267, 90, 127, 162, 244, 263, 155, 256, 62] chunk 29 optimal weight: 0.8980 chunk 330 optimal weight: 0.7980 chunk 267 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 244 optimal weight: 0.2980 chunk 263 optimal weight: 0.9980 chunk 155 optimal weight: 0.0020 chunk 256 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN A 156 GLN A 165 GLN A 444 ASN A 593 GLN B 593 GLN B 695 ASN B1139 ASN C 27 ASN C 593 GLN C 606 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.149452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116022 restraints weight = 31074.052| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.91 r_work: 0.3054 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28140 Z= 0.089 Angle : 0.433 6.564 38358 Z= 0.242 Chirality : 0.042 0.144 4320 Planarity : 0.004 0.068 4938 Dihedral : 4.069 38.220 3826 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.92 % Allowed : 11.25 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3489 helix: 1.87 (0.21), residues: 732 sheet: 0.48 (0.18), residues: 759 loop : -1.00 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 999 TYR 0.011 0.001 TYR C 633 PHE 0.014 0.001 PHE A 407 TRP 0.012 0.001 TRP B 460 HIS 0.003 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.09 (28077) covalent geometry : angle 0.43230 / 0.24 (38232) SS BOND : bond 0.00192 / 0.12 ( 63) SS BOND : angle 0.69560 / 0.49 ( 126) hydrogen bonds : bond 0.05023 / 3.37 ( 1032) hydrogen bonds : angle 4.71710 / 3.25 ( 2931) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 272 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7917 (mmm) REVERT: A 219 GLU cc_start: 0.8486 (tt0) cc_final: 0.8215 (tm-30) REVERT: A 344 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8307 (t0) REVERT: A 352 LYS cc_start: 0.8917 (ptpt) cc_final: 0.8693 (ttpp) REVERT: A 463 ARG cc_start: 0.8576 (ttt180) cc_final: 0.8319 (ttt90) REVERT: A 714 ASN cc_start: 0.7336 (OUTLIER) cc_final: 0.6912 (m110) REVERT: A 720 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7736 (mp10) REVERT: A 746 GLN cc_start: 0.8191 (mt0) cc_final: 0.7915 (tt0) REVERT: A 799 GLU cc_start: 0.8504 (tt0) cc_final: 0.8142 (mt-10) REVERT: A 833 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7991 (t0) REVERT: A 889 PHE cc_start: 0.7130 (p90) cc_final: 0.6420 (m-80) REVERT: A 1015 LYS cc_start: 0.7459 (mmtt) cc_final: 0.7083 (mptt) REVERT: A 1165 LYS cc_start: 0.8046 (mttt) cc_final: 0.7651 (mtpm) REVERT: A 1198 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7786 (mtt) REVERT: A 1232 MET cc_start: 0.6458 (mmt) cc_final: 0.4886 (pmm) REVERT: B 78 MET cc_start: 0.8304 (mmt) cc_final: 0.7455 (mmt) REVERT: B 201 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.6825 (ttt180) REVERT: B 219 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: B 463 ARG cc_start: 0.8441 (ttt180) cc_final: 0.8205 (ttp80) REVERT: B 517 ASN cc_start: 0.4144 (OUTLIER) cc_final: 0.3335 (t0) REVERT: B 522 CYS cc_start: 0.6979 (m) cc_final: 0.6631 (m) REVERT: B 698 GLU cc_start: 0.8395 (pt0) cc_final: 0.7960 (pt0) REVERT: B 720 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7702 (mp10) REVERT: B 746 GLN cc_start: 0.8119 (mt0) cc_final: 0.7882 (tt0) REVERT: B 775 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8181 (mtm180) REVERT: B 799 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7886 (mt-10) REVERT: B 884 LYS cc_start: 0.8134 (mttt) cc_final: 0.7836 (mttp) REVERT: B 885 ASP cc_start: 0.5361 (m-30) cc_final: 0.5049 (m-30) REVERT: B 966 ASN cc_start: 0.8388 (m-40) cc_final: 0.7985 (m-40) REVERT: B 1165 LYS cc_start: 0.8077 (mttt) cc_final: 0.7792 (ttmt) REVERT: B 1218 MET cc_start: 0.7215 (mtm) cc_final: 0.6983 (mtm) REVERT: B 1224 ASN cc_start: 0.5803 (OUTLIER) cc_final: 0.5231 (p0) REVERT: B 1232 MET cc_start: 0.6456 (mmt) cc_final: 0.4534 (pmm) REVERT: C 168 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8051 (mmm) REVERT: C 279 ASN cc_start: 0.8720 (p0) cc_final: 0.8483 (p0) REVERT: C 538 ASP cc_start: 0.7674 (p0) cc_final: 0.7318 (p0) REVERT: C 541 THR cc_start: 0.7210 (m) cc_final: 0.6729 (p) REVERT: C 698 GLU cc_start: 0.8199 (pt0) cc_final: 0.7893 (pt0) REVERT: C 746 GLN cc_start: 0.8259 (mt0) cc_final: 0.7865 (tt0) REVERT: C 775 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8323 (mtm180) REVERT: C 889 PHE cc_start: 0.6951 (p90) cc_final: 0.6316 (m-10) REVERT: C 1015 LYS cc_start: 0.7497 (mmtt) cc_final: 0.7003 (mtpm) REVERT: C 1104 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7328 (mt0) REVERT: C 1165 LYS cc_start: 0.7965 (mttt) cc_final: 0.7627 (mtpm) REVERT: C 1198 MET cc_start: 0.8399 (mtp) cc_final: 0.7681 (mtt) REVERT: C 1224 ASN cc_start: 0.6037 (OUTLIER) cc_final: 0.5048 (p0) REVERT: C 1232 MET cc_start: 0.6405 (mmt) cc_final: 0.4829 (pmm) outliers start: 59 outliers final: 31 residues processed: 316 average time/residue: 0.5426 time to fit residues: 206.4239 Evaluate side-chains 309 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 720 GLN Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1104 GLN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 872 SER Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 759 ASP Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 1005 VAL Chi-restraints excluded: chain C residue 1104 GLN Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1224 ASN Chi-restraints excluded: chain C residue 1226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [256, 116, 233, 194, 195, 305, 345, 328, 261, 262, 58] chunk 256 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 345 optimal weight: 2.9990 chunk 328 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 262 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 165 GLN A 444 ASN A 593 GLN A1054 ASN B 593 GLN B 695 ASN B1139 ASN C 27 ASN C 593 GLN C1054 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.145598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.110988 restraints weight = 31074.082| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.96 r_work: 0.2988 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28140 Z= 0.161 Angle : 0.534 7.550 38358 Z= 0.293 Chirality : 0.045 0.145 4320 Planarity : 0.005 0.073 4938 Dihedral : 4.396 38.449 3824 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.09 % Allowed : 11.19 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3489 helix: 1.57 (0.20), residues: 732 sheet: 0.51 (0.18), residues: 753 loop : -1.13 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1133 TYR 0.020 0.002 TYR B 633 PHE 0.015 0.002 PHE A 122 TRP 0.014 0.002 TRP C 188 HIS 0.008 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (28077) covalent geometry : angle 0.53074 / 0.29 (38232) SS BOND : bond 0.00334 / 0.21 ( 63) SS BOND : angle 1.13627 / 0.78 ( 126) hydrogen bonds : bond 0.06612 / 4.44 ( 1032) hydrogen bonds : angle 4.96144 / 3.41 ( 2931) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 263 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7926 (mmm) REVERT: A 219 GLU cc_start: 0.8524 (tt0) cc_final: 0.8286 (tm-30) REVERT: A 344 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8311 (t0) REVERT: A 352 LYS cc_start: 0.8994 (ptpt) cc_final: 0.8764 (ttpp) REVERT: A 463 ARG cc_start: 0.8610 (ttt180) cc_final: 0.8337 (ttt90) REVERT: A 714 ASN cc_start: 0.7464 (OUTLIER) cc_final: 0.7030 (m110) REVERT: A 720 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7744 (mp10) REVERT: A 746 GLN cc_start: 0.8178 (mt0) cc_final: 0.7887 (tt0) REVERT: A 833 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8179 (t0) REVERT: A 1015 LYS cc_start: 0.7569 (mmtt) cc_final: 0.7162 (mptt) REVERT: A 1104 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.6762 (mt0) REVERT: A 1165 LYS cc_start: 0.8112 (mttt) cc_final: 0.7717 (mtpm) REVERT: A 1198 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7849 (mtt) REVERT: A 1232 MET cc_start: 0.6419 (mmt) cc_final: 0.4861 (pmm) REVERT: B 120 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8701 (p) REVERT: B 219 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: B 463 ARG cc_start: 0.8485 (ttt180) cc_final: 0.8194 (ttt180) REVERT: B 517 ASN cc_start: 0.4263 (OUTLIER) cc_final: 0.3372 (t0) REVERT: B 522 CYS cc_start: 0.6978 (m) cc_final: 0.6596 (m) REVERT: B 559 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: B 698 GLU cc_start: 0.8490 (pt0) cc_final: 0.8050 (pt0) REVERT: B 720 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: B 739 ASN cc_start: 0.7910 (t0) cc_final: 0.7659 (t160) REVERT: B 746 GLN cc_start: 0.8165 (mt0) cc_final: 0.7928 (tt0) REVERT: B 775 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7605 (ptm-80) REVERT: B 799 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7982 (mt-10) REVERT: B 884 LYS cc_start: 0.8202 (mttt) cc_final: 0.7895 (mttp) REVERT: B 885 ASP cc_start: 0.5743 (m-30) cc_final: 0.5504 (m-30) REVERT: B 966 ASN cc_start: 0.8504 (m-40) cc_final: 0.8144 (m-40) REVERT: B 1165 LYS cc_start: 0.8133 (mttt) cc_final: 0.7834 (ttmt) REVERT: B 1218 MET cc_start: 0.7292 (mtm) cc_final: 0.6705 (mtt) REVERT: B 1224 ASN cc_start: 0.5825 (OUTLIER) cc_final: 0.5201 (p0) REVERT: B 1232 MET cc_start: 0.6509 (mmt) cc_final: 0.4551 (pmm) REVERT: C 168 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7975 (mmm) REVERT: C 219 GLU cc_start: 0.8379 (tt0) cc_final: 0.8156 (tt0) REVERT: C 462 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7950 (mmtm) REVERT: C 538 ASP cc_start: 0.7949 (p0) cc_final: 0.7580 (p0) REVERT: C 541 THR cc_start: 0.7247 (m) cc_final: 0.6764 (p) REVERT: C 698 GLU cc_start: 0.8373 (pt0) cc_final: 0.8140 (pt0) REVERT: C 720 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: C 746 GLN cc_start: 0.8286 (mt0) cc_final: 0.7899 (tt0) REVERT: C 775 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7833 (ptm-80) REVERT: C 889 PHE cc_start: 0.6993 (p90) cc_final: 0.6351 (m-10) REVERT: C 1015 LYS cc_start: 0.7608 (mmtt) cc_final: 0.7123 (mtpm) REVERT: C 1104 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.6865 (mt0) REVERT: C 1165 LYS cc_start: 0.8015 (mttt) cc_final: 0.7704 (mtpm) REVERT: C 1198 MET cc_start: 0.8345 (mtp) cc_final: 0.7695 (mtt) REVERT: C 1224 ASN cc_start: 0.5967 (OUTLIER) cc_final: 0.5022 (p0) REVERT: C 1232 MET cc_start: 0.6455 (mmt) cc_final: 0.4877 (pmm) outliers start: 64 outliers final: 35 residues processed: 306 average time/residue: 0.5318 time to fit residues: 195.3266 Evaluate side-chains 316 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 720 GLN Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1104 GLN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 720 GLN Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 872 SER Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1224 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 344 ASN Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 720 GLN Chi-restraints excluded: chain C residue 759 ASP Chi-restraints excluded: chain C residue 775 ARG Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 1005 VAL Chi-restraints excluded: chain C residue 1104 GLN Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1224 ASN Chi-restraints excluded: chain C residue 1226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [325, 104, 28, 57, 340, 92, 37, 315, 257, 297, 299] chunk 325 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 28 optimal weight: 0.0020 chunk 57 optimal weight: 5.9990 chunk 340 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 315 optimal weight: 2.9990 chunk 257 optimal weight: 8.9990 chunk 297 optimal weight: 3.9990 chunk 299 optimal weight: 4.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 165 GLN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 GLN A1054 ASN B 593 GLN B 695 ASN B1139 ASN C 593 GLN C1194 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.145638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.111436 restraints weight = 30999.006| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.92 r_work: 0.2993 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.277 28140 Z= 0.232 Angle : 0.727 59.200 38358 Z= 0.436 Chirality : 0.047 0.664 4320 Planarity : 0.005 0.171 4938 Dihedral : 4.446 38.441 3824 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.96 % Allowed : 11.32 % Favored : 86.73 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3489 helix: 1.55 (0.20), residues: 732 sheet: 0.50 (0.18), residues: 753 loop : -1.14 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1133 TYR 0.020 0.002 TYR B 633 PHE 0.015 0.002 PHE B 776 TRP 0.015 0.002 TRP C 188 HIS 0.007 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 (28077) covalent geometry : angle 0.72105 / 0.43 (38232) SS BOND : bond 0.00347 / 0.21 ( 63) SS BOND : angle 1.74995 / 1.11 ( 126) hydrogen bonds : bond 0.06649 / 4.46 ( 1032) hydrogen bonds : angle 4.97665 / 3.42 ( 2931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8906.67 seconds wall clock time: 152 minutes 3.35 seconds (9123.35 seconds total)