Starting phenix.real_space_refine on Wed Oct 28 10:38:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y6g_72561/10_2026/9y6g_72561.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y6g_72561/10_2026/9y6g_72561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y6g_72561/10_2026/9y6g_72561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y6g_72561/10_2026/9y6g_72561.map" model { file = "/net/cci-nas-00/data/ceres_data/9y6g_72561/10_2026/9y6g_72561.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y6g_72561/10_2026/9y6g_72561.cif" } resolution = 3.83 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= 0.001 sd= 0.042 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 51 residue(s): 0.02s 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: 5.86, per 1000 atoms: 0.21 Number of scatterers: 27450 At special positions: 0 Unit cell: (147.2, 157.55, 164.45, 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=2.03 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=2.03 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=2.03 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=2.04 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=2.02 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=2.04 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: 1.91 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 92 helices and 72 sheets defined 25.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 89 through 92 removed outlier: 3.925A 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 removed outlier: 3.538A pdb=" N THR A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 371 through 379 removed outlier: 4.132A pdb=" N SER A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.726A pdb=" N LYS A 393 " --> pdb=" O ASP A 390 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A 394 " --> pdb=" O ALA A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 394' 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 461 through 465 removed outlier: 3.826A pdb=" N GLY A 465 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 Processing helix 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 716 Processing helix chain 'A' and resid 825 through 831 Processing helix chain 'A' and resid 834 through 841 removed outlier: 3.710A pdb=" N GLN A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 874 removed outlier: 3.769A pdb=" N CYS A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 885 removed outlier: 3.569A pdb=" N ASP A 885 " --> pdb=" O LYS A 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 882 through 885' Processing helix chain 'A' and resid 914 through 922 Processing helix chain 'A' and resid 927 through 937 removed outlier: 3.557A pdb=" N ASN A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 940 No H-bonds generated for 'chain 'A' and resid 938 through 940' 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 Processing helix chain 'A' and resid 1006 through 1011 removed outlier: 4.044A pdb=" N LEU A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A1011 " --> pdb=" O MET A1007 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1006 through 1011' Processing helix chain 'A' and resid 1013 through 1031 Processing helix chain 'A' and resid 1036 through 1058 Processing helix chain 'A' and resid 1059 through 1062 Processing helix chain 'A' and resid 1070 through 1076 Processing helix chain 'A' and resid 1079 through 1127 removed outlier: 3.726A pdb=" N ALA A1085 " --> pdb=" O LEU A1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 removed outlier: 3.871A 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 177 through 181 removed outlier: 3.593A pdb=" N GLY B 181 " --> pdb=" O PRO B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.538A pdb=" N THR B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 371 through 379 removed outlier: 3.516A pdb=" N LEU B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 removed outlier: 3.792A pdb=" N LYS B 393 " --> pdb=" O ASP B 390 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE B 394 " --> pdb=" O ALA B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 390 through 394' 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 461 through 465 removed outlier: 3.838A pdb=" N GLY B 465 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 568 through 571 Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 707 through 716 Processing helix chain 'B' and resid 825 through 831 Processing helix chain 'B' and resid 834 through 841 removed outlier: 3.679A pdb=" N GLN B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 874 removed outlier: 3.827A pdb=" N CYS B 848 " --> pdb=" O TYR B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 885 removed outlier: 3.581A pdb=" N ASP B 885 " --> pdb=" O LYS B 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 882 through 885' Processing helix chain 'B' and resid 914 through 922 Processing helix chain 'B' and resid 927 through 937 removed outlier: 3.582A pdb=" N ASN B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 940 No H-bonds generated for 'chain 'B' and resid 938 through 940' Processing helix chain 'B' and resid 946 through 954 Processing helix chain 'B' and resid 964 through 978 Processing helix chain 'B' and resid 991 through 1002 Processing helix chain 'B' and resid 1006 through 1011 removed outlier: 4.100A pdb=" N LEU B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER B1011 " --> pdb=" O MET B1007 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1006 through 1011' Processing helix chain 'B' and resid 1013 through 1031 Processing helix chain 'B' and resid 1032 through 1034 No H-bonds generated for 'chain 'B' and resid 1032 through 1034' Processing helix chain 'B' and resid 1036 through 1058 Processing helix chain 'B' and resid 1059 through 1062 Processing helix chain 'B' and resid 1070 through 1076 Processing helix chain 'B' and resid 1079 through 1127 removed outlier: 3.675A pdb=" N ALA B1085 " --> pdb=" O LEU B1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 92 removed outlier: 3.940A 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 removed outlier: 3.531A pdb=" N GLY C 181 " --> pdb=" O PRO C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 303 removed outlier: 3.531A pdb=" N THR C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 371 through 379 removed outlier: 3.555A pdb=" N LEU C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 394 removed outlier: 3.711A pdb=" N LYS C 393 " --> pdb=" O ASP C 390 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE C 394 " --> pdb=" O ALA C 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 390 through 394' 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 459 through 464 removed outlier: 3.524A 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 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 716 Processing helix chain 'C' and resid 825 through 831 Processing helix chain 'C' and resid 834 through 841 removed outlier: 3.697A pdb=" N GLN C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 874 removed outlier: 3.751A pdb=" N CYS C 848 " --> pdb=" O TYR C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 885 removed outlier: 3.601A pdb=" N ASP C 885 " --> pdb=" O LYS C 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 882 through 885' Processing helix chain 'C' and resid 914 through 922 Processing helix chain 'C' and resid 927 through 937 removed outlier: 3.549A pdb=" N ASN C 937 " --> pdb=" O GLU C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 940 No H-bonds generated for 'chain 'C' and resid 938 through 940' Processing helix chain 'C' and resid 946 through 954 Processing helix chain 'C' and resid 964 through 978 Processing helix chain 'C' and resid 991 through 1002 Processing helix chain 'C' and resid 1006 through 1011 removed outlier: 4.058A pdb=" N LEU C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER C1011 " --> pdb=" O MET C1007 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1006 through 1011' Processing helix chain 'C' and resid 1013 through 1031 Processing helix chain 'C' and resid 1032 through 1034 No H-bonds generated for 'chain 'C' and resid 1032 through 1034' Processing helix chain 'C' and resid 1036 through 1058 Processing helix chain 'C' and resid 1059 through 1062 Processing helix chain 'C' and resid 1070 through 1076 Processing helix chain 'C' and resid 1079 through 1127 removed outlier: 3.509A pdb=" N ALA C1083 " --> pdb=" O ASP C1079 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C1085 " --> pdb=" O LEU C1081 " (cutoff:3.500A) 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: 7.833A pdb=" N ASP A 39 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR A 75 " --> pdb=" O ASP A 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 50 removed outlier: 7.569A pdb=" N THR A 49 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N PHE A 236 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ALA A 225 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN A 239 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE A 223 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 219 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR A 217 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 213 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 216 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 63 through 68 removed outlier: 3.504A pdb=" N GLY A 66 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 270 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN A 286 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.557A pdb=" N THR A 174 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.741A pdb=" N SER A 97 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 249 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY A 157 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 205 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 199 " --> pdb=" O VAL A 163 " (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 removed outlier: 3.507A pdb=" N LEU A 701 " --> pdb=" O VAL A 735 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 735 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 727 " --> pdb=" O VAL A 734 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AB1, first strand: chain 'A' and resid 331 through 335 removed outlier: 5.848A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 668 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 355 removed outlier: 3.669A pdb=" N VAL A 354 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 453 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 365 removed outlier: 4.085A pdb=" N GLU A 361 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS A 406 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 407 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 438 " --> pdb=" O ASN A 387 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASN A 444 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA A 381 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 369 through 370 removed outlier: 3.544A pdb=" N PHE A 370 " --> pdb=" O CYS A 614 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 484 through 488 removed outlier: 3.657A pdb=" N ASP A 589 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 487 " --> pdb=" O SER A 587 " (cutoff:3.500A) 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 565 through 566 Processing sheet with id=AB8, first strand: chain 'A' and resid 739 through 745 removed outlier: 8.778A pdb=" N PHE A 776 " --> pdb=" O THR A 741 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE A 743 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 778 " --> pdb=" O ILE A 743 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY A 753 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 758 " --> pdb=" O THR A 751 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR A 751 " --> pdb=" O VAL A 758 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 785 through 787 removed outlier: 6.110A pdb=" N ASN A 785 " --> pdb=" O LEU B 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 798 through 803 Processing sheet with id=AC2, first strand: chain 'A' and resid 806 through 816 removed outlier: 3.622A pdb=" N GLY A1153 " --> pdb=" O ALA A1150 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A1159 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A1144 " --> pdb=" O PHE A1159 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR A1161 " --> pdb=" O HIS A1142 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS A1142 " --> pdb=" O TYR A1161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 821 through 824 removed outlier: 4.411A pdb=" N LYS A 821 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 878 through 880 Processing sheet with id=AC5, first strand: chain 'A' and resid 890 through 891 Processing sheet with id=AC6, first strand: chain 'A' and resid 1175 through 1176 removed outlier: 3.854A pdb=" N LEU A1175 " --> pdb=" O ILE A1183 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A1183 " --> pdb=" O LEU A1175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 1191 through 1193 Processing sheet with id=AC8, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AC9, first strand: chain 'B' and resid 36 through 40 removed outlier: 7.856A pdb=" N ASP B 39 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR B 75 " --> pdb=" O ASP B 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.525A pdb=" N GLY B 66 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 270 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN B 286 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.609A pdb=" N THR B 174 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.736A pdb=" N SER B 97 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR B 249 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY B 157 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR B 205 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 199 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 235 through 241 removed outlier: 7.282A pdb=" N ALA B 225 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASN B 239 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE B 223 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 219 " --> pdb=" O THR B 222 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR B 217 " --> pdb=" O TYR B 224 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR B 213 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 216 " --> pdb=" O ILE B 103 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AD6, first strand: chain 'B' and resid 310 through 313 removed outlier: 3.515A pdb=" N LEU B 701 " --> pdb=" O VAL B 735 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 735 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 727 " --> pdb=" O VAL B 734 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AD8, first strand: chain 'B' and resid 332 through 335 removed outlier: 6.950A pdb=" N VAL B 333 " --> pdb=" O ASP B 634 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 669 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY B 668 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 353 through 355 removed outlier: 3.547A pdb=" N VAL B 354 " --> pdb=" O SER B 451 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER B 453 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 361 through 365 removed outlier: 4.076A pdb=" N GLU B 361 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B 406 " --> pdb=" O GLU B 361 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 407 " --> pdb=" O PHE B 600 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 438 " --> pdb=" O ASN B 387 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 361 through 365 removed outlier: 4.076A pdb=" N GLU B 361 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B 406 " --> pdb=" O GLU B 361 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 407 " --> pdb=" O PHE B 600 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 596 " --> pdb=" O GLN B 593 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 369 through 370 removed outlier: 3.530A 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 removed outlier: 3.664A pdb=" N ASP B 589 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B 487 " --> pdb=" O SER B 587 " (cutoff:3.500A) 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 565 through 566 Processing sheet with id=AE7, first strand: chain 'B' and resid 739 through 745 removed outlier: 8.840A pdb=" N PHE B 776 " --> pdb=" O THR B 741 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 743 " --> pdb=" O PHE B 776 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY B 753 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 758 " --> pdb=" O THR B 751 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N THR B 751 " --> pdb=" O VAL B 758 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 785 through 787 removed outlier: 6.021A pdb=" N ASN B 785 " --> pdb=" O LEU C 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'B' and resid 798 through 803 Processing sheet with id=AF1, first strand: chain 'B' and resid 806 through 816 removed outlier: 3.645A pdb=" N GLY B1153 " --> pdb=" O ALA B1150 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B1159 " --> pdb=" O ILE B1144 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE B1144 " --> pdb=" O PHE B1159 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N TYR B1161 " --> pdb=" O HIS B1142 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS B1142 " --> pdb=" O TYR B1161 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 821 through 824 removed outlier: 4.398A pdb=" N LYS B 821 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 890 through 891 Processing sheet with id=AF4, first strand: chain 'B' and resid 1175 through 1176 removed outlier: 3.839A pdb=" N LEU B1175 " --> pdb=" O ILE B1183 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 1188 through 1193 removed outlier: 3.990A pdb=" N THR B1200 " --> pdb=" O TYR B1189 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AF7, first strand: chain 'C' and resid 36 through 40 removed outlier: 7.785A pdb=" N ASP C 39 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR C 75 " --> pdb=" O ASP C 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 49 through 50 removed outlier: 7.444A pdb=" N THR C 49 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N PHE C 236 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE C 236 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N PHE C 227 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 238 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU C 219 " --> pdb=" O THR C 222 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR C 217 " --> pdb=" O TYR C 224 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR C 213 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 216 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 63 through 68 removed outlier: 3.573A pdb=" N THR C 270 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 3.968A 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: 6.610A pdb=" N THR C 174 " --> pdb=" O THR C 255 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.713A pdb=" N SER C 97 " --> pdb=" O TYR C 249 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR C 249 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY C 157 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR C 205 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 199 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AG4, first strand: chain 'C' and resid 310 through 313 removed outlier: 3.526A pdb=" N LEU C 701 " --> pdb=" O VAL C 735 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 735 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE C 727 " --> pdb=" O VAL C 734 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AG6, first strand: chain 'C' and resid 331 through 335 removed outlier: 3.554A pdb=" N PHE C 669 " --> pdb=" O PHE C 678 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N TYR C 667 " --> pdb=" O ILE C 680 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 353 through 355 removed outlier: 3.516A pdb=" N VAL C 354 " --> pdb=" O SER C 451 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER C 453 " --> pdb=" O VAL C 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'C' and resid 361 through 365 removed outlier: 4.159A pdb=" N GLU C 361 " --> pdb=" O LYS C 406 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS C 406 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER C 401 " --> pdb=" O HIS C 606 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 407 " --> pdb=" O PHE C 600 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 438 " --> pdb=" O ASN C 387 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASN C 444 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA C 381 " --> pdb=" O ASN C 444 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 369 through 370 removed outlier: 3.516A pdb=" N PHE C 370 " --> pdb=" O CYS C 614 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 484 through 488 removed outlier: 3.696A pdb=" N ASP C 589 " --> pdb=" O VAL C 485 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR C 487 " --> pdb=" O SER C 587 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 492 through 493 Processing sheet with id=AH3, first strand: chain 'C' and resid 565 through 566 Processing sheet with id=AH4, first strand: chain 'C' and resid 739 through 745 removed outlier: 8.784A pdb=" N PHE C 776 " --> pdb=" O THR C 741 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE C 743 " --> pdb=" O PHE C 776 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN C 778 " --> pdb=" O ILE C 743 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY C 753 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 758 " --> pdb=" O THR C 751 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N THR C 751 " --> pdb=" O VAL C 758 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 798 through 816 removed outlier: 6.791A pdb=" N LYS C1165 " --> pdb=" O SER C 804 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE C 806 " --> pdb=" O PRO C1163 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 808 " --> pdb=" O TYR C1161 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR C1161 " --> pdb=" O ILE C 808 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN C 810 " --> pdb=" O PHE C1159 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE C1159 " --> pdb=" O ASN C 810 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL C 812 " --> pdb=" O ILE C1157 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE C1157 " --> pdb=" O VAL C 812 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE C 814 " --> pdb=" O TYR C1155 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR C1155 " --> pdb=" O PHE C 814 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLN C 816 " --> pdb=" O GLY C1153 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY C1153 " --> pdb=" O GLN C 816 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C1153 " --> pdb=" O ALA C1150 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C1159 " --> pdb=" O ILE C1144 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C1144 " --> pdb=" O PHE C1159 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR C1161 " --> pdb=" O HIS C1142 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N HIS C1142 " --> pdb=" O TYR C1161 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 821 through 824 removed outlier: 4.478A pdb=" N LYS C 821 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 890 through 891 Processing sheet with id=AH8, first strand: chain 'C' and resid 1175 through 1176 removed outlier: 3.902A pdb=" N LEU C1175 " --> pdb=" O ILE C1183 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C1183 " --> pdb=" O LEU C1175 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 1188 through 1193 removed outlier: 4.040A pdb=" N THR C1200 " --> pdb=" O TYR C1189 " (cutoff:3.500A) 981 hydrogen bonds defined for protein. 2691 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: 7.21 Time building geometry restraints manager: 2.69 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: 8831 1.34 - 1.47: 7047 1.47 - 1.59: 11962 1.59 - 1.71: 0 1.71 - 1.84: 237 Bond restraints: 28077 Sorted by residual: bond pdb=" CA ILE C1143 " pdb=" CB ILE C1143 " ideal model delta sigma weight residual 1.545 1.535 0.010 9.10e-03 1.21e+04 1.23e+00 bond pdb=" CB PRO B 898 " pdb=" CG PRO B 898 " ideal model delta sigma weight residual 1.492 1.441 0.051 5.00e-02 4.00e+02 1.03e+00 bond pdb=" CB PRO A 898 " pdb=" CG PRO A 898 " ideal model delta sigma weight residual 1.492 1.442 0.050 5.00e-02 4.00e+02 9.84e-01 bond pdb=" C ASN B 517 " pdb=" N GLY B 518 " ideal model delta sigma weight residual 1.330 1.343 -0.012 1.27e-02 6.20e+03 9.58e-01 bond pdb=" N ILE B 409 " pdb=" CA ILE B 409 " ideal model delta sigma weight residual 1.468 1.458 0.010 1.05e-02 9.07e+03 9.17e-01 ... (remaining 28072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 37336 1.61 - 3.21: 826 3.21 - 4.82: 62 4.82 - 6.43: 0 6.43 - 8.03: 8 Bond angle restraints: 38232 Sorted by residual: angle pdb=" N ILE A 724 " pdb=" CA ILE A 724 " pdb=" C ILE A 724 " ideal model delta sigma weight residual 112.96 109.10 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" C ASN B 387 " pdb=" N ASN B 388 " pdb=" CA ASN B 388 " ideal model delta sigma weight residual 121.54 128.40 -6.86 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C ASN C 387 " pdb=" N ASN C 388 " pdb=" CA ASN C 388 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C ASN A 387 " pdb=" N ASN A 388 " pdb=" CA ASN A 388 " ideal model delta sigma weight residual 121.54 128.20 -6.66 1.91e+00 2.74e-01 1.22e+01 angle pdb=" N GLY B 316 " pdb=" CA GLY B 316 " pdb=" C GLY B 316 " ideal model delta sigma weight residual 113.18 121.21 -8.03 2.37e+00 1.78e-01 1.15e+01 ... (remaining 38227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.40: 15162 14.40 - 28.79: 1186 28.79 - 43.19: 273 43.19 - 57.58: 90 57.58 - 71.98: 23 Dihedral angle restraints: 16734 sinusoidal: 6429 harmonic: 10305 Sorted by residual: dihedral pdb=" CA ASN B 315 " pdb=" C ASN B 315 " pdb=" N GLY B 316 " pdb=" CA GLY B 316 " ideal model delta harmonic sigma weight residual 180.00 151.42 28.58 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ASN A 315 " pdb=" C ASN A 315 " pdb=" N GLY A 316 " pdb=" CA GLY A 316 " ideal model delta harmonic sigma weight residual 180.00 151.63 28.37 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ASN C 315 " pdb=" C ASN C 315 " pdb=" N GLY C 316 " pdb=" CA GLY C 316 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 16731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2461 0.030 - 0.060: 1095 0.060 - 0.091: 468 0.091 - 0.121: 241 0.121 - 0.151: 55 Chirality restraints: 4320 Sorted by residual: chirality pdb=" CB ILE A 125 " pdb=" CA ILE A 125 " pdb=" CG1 ILE A 125 " pdb=" CG2 ILE A 125 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CB ILE C 125 " pdb=" CA ILE C 125 " pdb=" CG1 ILE C 125 " pdb=" CG2 ILE C 125 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CB ILE B 125 " pdb=" CA ILE B 125 " pdb=" CG1 ILE B 125 " pdb=" CG2 ILE B 125 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 4317 not shown) Planarity restraints: 4938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 897 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.03e+00 pdb=" N PRO C 898 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 898 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 898 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 897 " -0.044 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO B 898 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 898 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 898 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 897 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.08e+00 pdb=" N PRO A 898 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 898 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 898 " -0.035 5.00e-02 4.00e+02 ... (remaining 4935 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 8514 2.82 - 3.34: 21582 3.34 - 3.86: 43511 3.86 - 4.38: 47022 4.38 - 4.90: 85533 Nonbonded interactions: 206162 Sorted by model distance: nonbonded pdb=" O CYS B 938 " pdb=" OH TYR B 953 " model vdw 2.298 3.040 nonbonded pdb=" O CYS C 938 " pdb=" OH TYR C 953 " model vdw 2.307 3.040 nonbonded pdb=" O CYS A 938 " pdb=" OH TYR A 953 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR B 636 " pdb=" OD1 ASP B 671 " model vdw 2.317 3.040 nonbonded pdb=" O PRO C 523 " pdb=" OG1 THR C 526 " model vdw 2.337 3.040 ... (remaining 206157 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: 0.02 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 0.080 Set scattering table: 0.060 Process input model: 26.770 Find NCS groups from input model: 0.440 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28140 Z= 0.187 Angle : 0.583 8.033 38358 Z= 0.340 Chirality : 0.045 0.151 4320 Planarity : 0.005 0.071 4938 Dihedral : 11.663 71.977 9957 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.57 % Allowed : 5.25 % Favored : 90.18 % 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: -1.67 (0.13), residues: 3489 helix: -1.16 (0.16), residues: 747 sheet: -0.40 (0.19), residues: 735 loop : -1.36 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 76 TYR 0.017 0.002 TYR C1161 PHE 0.019 0.002 PHE B 122 TRP 0.006 0.001 TRP B 348 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (28077) covalent geometry : angle 0.58169 / 0.34 (38232) SS BOND : bond 0.00288 / 0.19 ( 63) SS BOND : angle 0.90721 / 0.61 ( 126) hydrogen bonds : bond 0.23729 / 15.79 ( 971) hydrogen bonds : angle 8.13095 / 5.43 ( 2691) *********************** 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 531 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 391 time to evaluate : 0.819 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 56 VAL cc_start: 0.9432 (OUTLIER) cc_final: 0.9165 (p) REVERT: A 78 MET cc_start: 0.9173 (mmm) cc_final: 0.8591 (mmm) REVERT: A 371 ASN cc_start: 0.5453 (OUTLIER) cc_final: 0.4902 (p0) REVERT: A 376 MET cc_start: 0.9050 (mtm) cc_final: 0.8733 (mtp) REVERT: A 387 ASN cc_start: 0.8337 (t0) cc_final: 0.8034 (t0) REVERT: A 716 SER cc_start: 0.9377 (m) cc_final: 0.8942 (p) REVERT: A 893 ASP cc_start: 0.8934 (m-30) cc_final: 0.8676 (t70) REVERT: A 917 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7518 (mt-10) REVERT: A 984 TRP cc_start: 0.8381 (m-90) cc_final: 0.7748 (m-10) REVERT: A 1054 ASN cc_start: 0.9253 (OUTLIER) cc_final: 0.8872 (m-40) REVERT: A 1092 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8538 (m-40) REVERT: A 1107 SER cc_start: 0.9481 (m) cc_final: 0.9055 (t) REVERT: B 56 VAL cc_start: 0.9486 (OUTLIER) cc_final: 0.9165 (m) REVERT: B 78 MET cc_start: 0.9143 (mmm) cc_final: 0.8650 (mmm) REVERT: B 233 VAL cc_start: 0.9250 (t) cc_final: 0.9035 (m) REVERT: B 295 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8676 (tmm) REVERT: B 371 ASN cc_start: 0.5344 (OUTLIER) cc_final: 0.4637 (p0) REVERT: B 546 TYR cc_start: 0.5532 (p90) cc_final: 0.4970 (p90) REVERT: B 716 SER cc_start: 0.9283 (m) cc_final: 0.8768 (p) REVERT: B 917 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7751 (mt-10) REVERT: B 956 ILE cc_start: 0.9426 (mt) cc_final: 0.9208 (tt) REVERT: B 984 TRP cc_start: 0.8125 (m-90) cc_final: 0.7543 (m-10) REVERT: B 1092 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8356 (t0) REVERT: B 1107 SER cc_start: 0.9446 (m) cc_final: 0.8890 (t) REVERT: C 56 VAL cc_start: 0.9479 (OUTLIER) cc_final: 0.9111 (m) REVERT: C 78 MET cc_start: 0.9025 (mmm) cc_final: 0.8391 (mmm) REVERT: C 118 MET cc_start: 0.7766 (ttp) cc_final: 0.7565 (ttm) REVERT: C 295 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8844 (tmm) REVERT: C 371 ASN cc_start: 0.5344 (OUTLIER) cc_final: 0.4748 (p0) REVERT: C 546 TYR cc_start: 0.6112 (p90) cc_final: 0.5411 (p90) REVERT: C 716 SER cc_start: 0.9349 (m) cc_final: 0.8919 (p) REVERT: C 840 GLN cc_start: 0.9262 (mm-40) cc_final: 0.8320 (mm-40) REVERT: C 893 ASP cc_start: 0.8755 (m-30) cc_final: 0.8438 (t70) REVERT: C 917 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7961 (mm-30) REVERT: C 984 TRP cc_start: 0.8238 (m-90) cc_final: 0.7667 (m-10) REVERT: C 1054 ASN cc_start: 0.9322 (OUTLIER) cc_final: 0.8913 (m-40) REVERT: C 1092 ASN cc_start: 0.8931 (OUTLIER) cc_final: 0.8590 (t0) REVERT: C 1106 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9062 (tt) REVERT: C 1107 SER cc_start: 0.9440 (m) cc_final: 0.9236 (m) outliers start: 140 outliers final: 51 residues processed: 514 average time/residue: 0.1549 time to fit residues: 133.1299 Evaluate side-chains 262 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 197 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1092 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 725 ASN Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 1092 ASN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 1054 ASN Chi-restraints excluded: chain C residue 1092 ASN Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1111 LEU Chi-restraints excluded: chain C residue 1130 GLN 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: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS A1130 GLN B 215 HIS B 840 GLN B1001 ASN B1130 GLN C 27 ASN C 215 HIS C 387 ASN C 461 ASN C 995 ASN C1130 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.095498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.074087 restraints weight = 65113.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.076511 restraints weight = 35015.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078153 restraints weight = 23283.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.079292 restraints weight = 17759.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.080025 restraints weight = 14787.679| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28140 Z= 0.128 Angle : 0.546 7.682 38358 Z= 0.295 Chirality : 0.043 0.221 4320 Planarity : 0.004 0.043 4938 Dihedral : 6.546 59.833 3907 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.56 % Allowed : 9.75 % Favored : 86.69 % Cbeta Deviations : 0.00 % 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: -0.97 (0.14), residues: 3489 helix: 0.24 (0.19), residues: 765 sheet: -0.27 (0.19), residues: 756 loop : -1.15 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 579 TYR 0.019 0.001 TYR C 211 PHE 0.014 0.001 PHE A 776 TRP 0.005 0.001 TRP A 348 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (28077) covalent geometry : angle 0.54337 / 0.29 (38232) SS BOND : bond 0.00265 / 0.14 ( 63) SS BOND : angle 1.15441 / 0.76 ( 126) hydrogen bonds : bond 0.04876 / 3.26 ( 971) hydrogen bonds : angle 5.92781 / 3.94 ( 2691) *********************** 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 341 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 232 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9003 (mmm) cc_final: 0.8589 (mmm) REVERT: A 295 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8333 (tmm) REVERT: A 716 SER cc_start: 0.9337 (m) cc_final: 0.8918 (p) REVERT: A 1001 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8797 (p0) REVERT: A 1007 MET cc_start: 0.6766 (mmm) cc_final: 0.6511 (mtt) REVERT: A 1054 ASN cc_start: 0.9195 (OUTLIER) cc_final: 0.8818 (m-40) REVERT: A 1107 SER cc_start: 0.9354 (m) cc_final: 0.9047 (t) REVERT: A 1218 MET cc_start: 0.4871 (tpt) cc_final: 0.4275 (tpt) REVERT: B 56 VAL cc_start: 0.9501 (OUTLIER) cc_final: 0.9191 (m) REVERT: B 78 MET cc_start: 0.8996 (mmm) cc_final: 0.8651 (mmm) REVERT: B 291 MET cc_start: 0.8522 (mmm) cc_final: 0.8231 (mmp) REVERT: B 371 ASN cc_start: 0.5547 (OUTLIER) cc_final: 0.5329 (p0) REVERT: B 387 ASN cc_start: 0.8389 (t0) cc_final: 0.7554 (t0) REVERT: B 388 ASN cc_start: 0.8904 (m-40) cc_final: 0.8170 (m-40) REVERT: B 394 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8875 (mt) REVERT: B 397 MET cc_start: 0.8218 (mtm) cc_final: 0.7994 (mtm) REVERT: B 546 TYR cc_start: 0.5388 (p90) cc_final: 0.5117 (p90) REVERT: B 716 SER cc_start: 0.9245 (m) cc_final: 0.8862 (p) REVERT: B 772 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7387 (m) REVERT: B 840 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.7716 (mm-40) REVERT: B 865 THR cc_start: 0.9483 (m) cc_final: 0.9282 (p) REVERT: B 917 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7804 (mt-10) REVERT: B 956 ILE cc_start: 0.9300 (mt) cc_final: 0.9095 (tt) REVERT: B 984 TRP cc_start: 0.8268 (m-90) cc_final: 0.7760 (m-10) REVERT: B 1092 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8428 (t0) REVERT: B 1107 SER cc_start: 0.9411 (m) cc_final: 0.8937 (t) REVERT: B 1232 MET cc_start: 0.6765 (tpt) cc_final: 0.6564 (tpt) REVERT: C 56 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9227 (p) REVERT: C 78 MET cc_start: 0.8939 (mmm) cc_final: 0.8516 (mmm) REVERT: C 295 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8548 (tmm) REVERT: C 394 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8986 (mt) REVERT: C 546 TYR cc_start: 0.5974 (p90) cc_final: 0.5601 (p90) REVERT: C 716 SER cc_start: 0.9324 (m) cc_final: 0.8930 (p) REVERT: C 984 TRP cc_start: 0.8331 (m-90) cc_final: 0.7891 (m-10) REVERT: C 1054 ASN cc_start: 0.9210 (OUTLIER) cc_final: 0.8855 (m-40) REVERT: C 1092 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8586 (t0) REVERT: C 1106 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9126 (tt) REVERT: C 1177 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6737 (pt) REVERT: C 1181 ARG cc_start: 0.7844 (mtm180) cc_final: 0.7434 (mtm180) outliers start: 109 outliers final: 49 residues processed: 322 average time/residue: 0.1482 time to fit residues: 81.7080 Evaluate side-chains 226 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 161 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1001 ASN Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 840 GLN Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1092 ASN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 733 CYS Chi-restraints excluded: chain C residue 738 TYR Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 811 MET Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 1054 ASN Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1092 ASN Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1111 LEU Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1177 ILE 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: 9.9990 chunk 248 optimal weight: 9.9990 chunk 190 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 286 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 HIS B1001 ASN C1001 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.092697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.071197 restraints weight = 66050.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.073604 restraints weight = 35341.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.075251 restraints weight = 23451.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.076343 restraints weight = 17821.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.076999 restraints weight = 14886.507| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 28140 Z= 0.237 Angle : 0.614 12.357 38358 Z= 0.327 Chirality : 0.045 0.364 4320 Planarity : 0.004 0.044 4938 Dihedral : 6.214 59.784 3872 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.98 % Allowed : 10.67 % Favored : 85.36 % Cbeta Deviations : 0.00 % 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: -0.80 (0.14), residues: 3489 helix: 0.79 (0.19), residues: 774 sheet: -0.35 (0.18), residues: 771 loop : -1.17 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 201 TYR 0.018 0.001 TYR C1206 PHE 0.033 0.002 PHE B 600 TRP 0.023 0.001 TRP C1197 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.24 (28077) covalent geometry : angle 0.60533 / 0.32 (38232) SS BOND : bond 0.00265 / 0.17 ( 63) SS BOND : angle 1.90450 / 1.45 ( 126) hydrogen bonds : bond 0.05035 / 3.38 ( 971) hydrogen bonds : angle 5.76933 / 3.85 ( 2691) *********************** 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 288 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 166 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9081 (mmm) cc_final: 0.8654 (mmm) REVERT: A 716 SER cc_start: 0.9345 (m) cc_final: 0.8936 (p) REVERT: A 1001 ASN cc_start: 0.9215 (OUTLIER) cc_final: 0.8591 (p0) REVERT: A 1054 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.8829 (m-40) REVERT: A 1107 SER cc_start: 0.9396 (m) cc_final: 0.9098 (t) REVERT: A 1197 TRP cc_start: 0.8590 (m100) cc_final: 0.8251 (m100) REVERT: A 1218 MET cc_start: 0.4973 (tpt) cc_final: 0.4701 (tpt) REVERT: B 56 VAL cc_start: 0.9477 (OUTLIER) cc_final: 0.9187 (m) REVERT: B 78 MET cc_start: 0.9112 (mmm) cc_final: 0.8893 (mmt) REVERT: B 295 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8960 (tpp) REVERT: B 387 ASN cc_start: 0.8401 (t0) cc_final: 0.7581 (t0) REVERT: B 388 ASN cc_start: 0.8973 (m-40) cc_final: 0.8338 (m110) REVERT: B 394 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8993 (mt) REVERT: B 397 MET cc_start: 0.8443 (mtm) cc_final: 0.8148 (mtm) REVERT: B 546 TYR cc_start: 0.5440 (p90) cc_final: 0.5138 (p90) REVERT: B 716 SER cc_start: 0.9351 (m) cc_final: 0.8934 (p) REVERT: B 865 THR cc_start: 0.9557 (OUTLIER) cc_final: 0.9345 (p) REVERT: B 917 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7964 (mt-10) REVERT: B 1092 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8545 (t0) REVERT: B 1107 SER cc_start: 0.9434 (m) cc_final: 0.8962 (t) REVERT: B 1232 MET cc_start: 0.6837 (tpt) cc_final: 0.6625 (tpt) REVERT: C 56 VAL cc_start: 0.9447 (OUTLIER) cc_final: 0.9228 (p) REVERT: C 78 MET cc_start: 0.9037 (mmm) cc_final: 0.8593 (mmm) REVERT: C 88 ARG cc_start: 0.8076 (mtt90) cc_final: 0.7648 (mtm-85) REVERT: C 546 TYR cc_start: 0.6027 (p90) cc_final: 0.5634 (p90) REVERT: C 716 SER cc_start: 0.9334 (m) cc_final: 0.8961 (p) REVERT: C 1054 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.8920 (m-40) REVERT: C 1092 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8699 (t0) REVERT: C 1106 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9066 (tt) REVERT: C 1177 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6774 (pt) REVERT: C 1181 ARG cc_start: 0.7785 (mtm180) cc_final: 0.7482 (mtm180) REVERT: C 1218 MET cc_start: 0.5611 (ppp) cc_final: 0.4357 (tmm) outliers start: 122 outliers final: 80 residues processed: 271 average time/residue: 0.1471 time to fit residues: 68.7140 Evaluate side-chains 243 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 151 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1001 ASN Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1208 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 840 GLN Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1092 ASN Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 733 CYS Chi-restraints excluded: chain C residue 738 TYR Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 811 MET Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain C residue 1054 ASN Chi-restraints excluded: chain C residue 1067 ILE Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1092 ASN Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1111 LEU Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1177 ILE 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: 1.9990 chunk 183 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 chunk 344 optimal weight: 0.8980 chunk 268 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 199 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1130 GLN B1001 ASN B1130 GLN C 426 GLN C 461 ASN C1001 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.095272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.073847 restraints weight = 64688.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.076329 restraints weight = 34261.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.077999 restraints weight = 22524.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.079151 restraints weight = 17043.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.079889 restraints weight = 14153.765| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 28140 Z= 0.098 Angle : 0.504 9.182 38358 Z= 0.269 Chirality : 0.042 0.258 4320 Planarity : 0.003 0.039 4938 Dihedral : 5.710 59.396 3869 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.03 % Allowed : 10.86 % Favored : 86.11 % Cbeta Deviations : 0.00 % 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: -0.51 (0.14), residues: 3489 helix: 1.28 (0.20), residues: 765 sheet: -0.21 (0.18), residues: 765 loop : -1.07 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 719 TYR 0.011 0.001 TYR A1225 PHE 0.027 0.001 PHE B 600 TRP 0.020 0.001 TRP C1197 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (28077) covalent geometry : angle 0.50115 / 0.27 (38232) SS BOND : bond 0.00270 / 0.17 ( 63) SS BOND : angle 1.11297 / 0.83 ( 126) hydrogen bonds : bond 0.04250 / 2.86 ( 971) hydrogen bonds : angle 5.34813 / 3.57 ( 2691) *********************** 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 269 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 176 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9034 (mmm) cc_final: 0.8648 (mmm) REVERT: A 372 MET cc_start: 0.8340 (mmm) cc_final: 0.8015 (mmm) REVERT: A 716 SER cc_start: 0.9224 (m) cc_final: 0.8802 (p) REVERT: A 1001 ASN cc_start: 0.9298 (p0) cc_final: 0.8903 (p0) REVERT: A 1054 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8834 (m-40) REVERT: A 1107 SER cc_start: 0.9297 (m) cc_final: 0.9037 (t) REVERT: A 1130 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7682 (mm-40) REVERT: A 1197 TRP cc_start: 0.8562 (m100) cc_final: 0.8092 (m100) REVERT: B 56 VAL cc_start: 0.9468 (OUTLIER) cc_final: 0.9152 (m) REVERT: B 78 MET cc_start: 0.9019 (mmm) cc_final: 0.8687 (mmm) REVERT: B 127 ILE cc_start: 0.9439 (mt) cc_final: 0.9220 (mt) REVERT: B 387 ASN cc_start: 0.8399 (t0) cc_final: 0.7647 (t0) REVERT: B 388 ASN cc_start: 0.8962 (m-40) cc_final: 0.8335 (m-40) REVERT: B 397 MET cc_start: 0.8402 (mtm) cc_final: 0.8068 (mtm) REVERT: B 546 TYR cc_start: 0.5241 (p90) cc_final: 0.4924 (p90) REVERT: B 716 SER cc_start: 0.9327 (m) cc_final: 0.8887 (p) REVERT: B 772 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7448 (m) REVERT: B 865 THR cc_start: 0.9540 (OUTLIER) cc_final: 0.9335 (p) REVERT: B 900 LEU cc_start: 0.9136 (tp) cc_final: 0.8851 (tt) REVERT: B 917 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7891 (mt-10) REVERT: B 1092 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8445 (t0) REVERT: B 1107 SER cc_start: 0.9381 (m) cc_final: 0.8927 (t) REVERT: B 1232 MET cc_start: 0.6795 (tpt) cc_final: 0.6585 (tpt) REVERT: C 78 MET cc_start: 0.8933 (mmm) cc_final: 0.8566 (mmm) REVERT: C 88 ARG cc_start: 0.8032 (mtt90) cc_final: 0.7620 (mtm-85) REVERT: C 397 MET cc_start: 0.7919 (mtm) cc_final: 0.7713 (mtm) REVERT: C 546 TYR cc_start: 0.5876 (p90) cc_final: 0.5503 (p90) REVERT: C 716 SER cc_start: 0.9205 (m) cc_final: 0.8875 (p) REVERT: C 1054 ASN cc_start: 0.9234 (OUTLIER) cc_final: 0.8848 (m-40) REVERT: C 1092 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8619 (t0) REVERT: C 1106 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9021 (tt) REVERT: C 1181 ARG cc_start: 0.7788 (mtm180) cc_final: 0.7477 (mtm180) outliers start: 93 outliers final: 53 residues processed: 259 average time/residue: 0.1456 time to fit residues: 64.7392 Evaluate side-chains 219 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 157 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1092 ASN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 708 CYS Chi-restraints excluded: chain C residue 738 TYR Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 811 MET Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 1054 ASN Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1092 ASN Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1111 LEU 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: 10.0000 chunk 214 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 279 optimal weight: 6.9990 chunk 282 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 345 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1130 GLN B 344 ASN ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 995 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1001 ASN C 25 ASN ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 715 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.091657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.070342 restraints weight = 66103.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.072677 restraints weight = 36065.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.074262 restraints weight = 24223.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.075321 restraints weight = 18573.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.076033 restraints weight = 15554.052| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 28140 Z= 0.260 Angle : 0.616 10.440 38358 Z= 0.326 Chirality : 0.045 0.259 4320 Planarity : 0.004 0.042 4938 Dihedral : 5.846 59.562 3858 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.82 % Allowed : 11.61 % Favored : 84.57 % Cbeta Deviations : 0.00 % 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: -0.66 (0.14), residues: 3489 helix: 1.30 (0.20), residues: 762 sheet: -0.62 (0.18), residues: 774 loop : -1.06 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 201 TYR 0.016 0.002 TYR A 442 PHE 0.024 0.002 PHE B 600 TRP 0.014 0.002 TRP C1197 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.26 (28077) covalent geometry : angle 0.61267 / 0.32 (38232) SS BOND : bond 0.00305 / 0.19 ( 63) SS BOND : angle 1.30306 / 0.93 ( 126) hydrogen bonds : bond 0.04790 / 3.22 ( 971) hydrogen bonds : angle 5.53562 / 3.71 ( 2691) *********************** 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 269 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 152 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9087 (mmm) cc_final: 0.8664 (mmm) REVERT: A 291 MET cc_start: 0.8890 (mmp) cc_final: 0.8621 (mmm) REVERT: A 295 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8548 (tmm) REVERT: A 372 MET cc_start: 0.8682 (mmm) cc_final: 0.8450 (mmm) REVERT: A 716 SER cc_start: 0.9216 (m) cc_final: 0.8810 (p) REVERT: A 1001 ASN cc_start: 0.9345 (p0) cc_final: 0.8954 (p0) REVERT: A 1054 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8851 (m-40) REVERT: A 1197 TRP cc_start: 0.8531 (m100) cc_final: 0.8212 (m100) REVERT: B 56 VAL cc_start: 0.9490 (OUTLIER) cc_final: 0.9205 (m) REVERT: B 78 MET cc_start: 0.9096 (mmm) cc_final: 0.8826 (mmt) REVERT: B 387 ASN cc_start: 0.8398 (t0) cc_final: 0.7627 (t0) REVERT: B 388 ASN cc_start: 0.8985 (m-40) cc_final: 0.8334 (m-40) REVERT: B 546 TYR cc_start: 0.5354 (p90) cc_final: 0.5020 (p90) REVERT: B 716 SER cc_start: 0.9341 (m) cc_final: 0.8914 (p) REVERT: B 772 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7511 (m) REVERT: B 900 LEU cc_start: 0.9244 (tp) cc_final: 0.9014 (tt) REVERT: B 917 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7883 (mt-10) REVERT: B 1092 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8587 (t0) REVERT: B 1232 MET cc_start: 0.6981 (tpt) cc_final: 0.6772 (tpt) REVERT: C 78 MET cc_start: 0.9023 (mmm) cc_final: 0.8685 (mmm) REVERT: C 88 ARG cc_start: 0.8009 (mtt90) cc_final: 0.7605 (mtm-85) REVERT: C 716 SER cc_start: 0.9206 (m) cc_final: 0.8818 (p) REVERT: C 1054 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8905 (m-40) REVERT: C 1092 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8814 (t0) outliers start: 117 outliers final: 79 residues processed: 255 average time/residue: 0.1460 time to fit residues: 63.9986 Evaluate side-chains 226 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 140 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 725 ASN Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 811 MET Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1092 ASN Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain B residue 1218 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 708 CYS Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 738 TYR Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 1054 ASN Chi-restraints excluded: chain C residue 1067 ILE Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1092 ASN Chi-restraints excluded: chain C residue 1111 LEU Chi-restraints excluded: chain C residue 1112 VAL 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: 2.9990 chunk 101 optimal weight: 0.8980 chunk 263 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 307 optimal weight: 2.9990 chunk 280 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 294 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1001 ASN C 995 ASN C1130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.094658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.073313 restraints weight = 64845.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.075737 restraints weight = 34906.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.077393 restraints weight = 23220.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.078483 restraints weight = 17697.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.079227 restraints weight = 14780.799| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 28140 Z= 0.098 Angle : 0.500 9.344 38358 Z= 0.266 Chirality : 0.042 0.230 4320 Planarity : 0.003 0.041 4938 Dihedral : 5.425 59.642 3854 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.87 % Allowed : 12.62 % Favored : 84.51 % 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: -0.47 (0.14), residues: 3489 helix: 1.65 (0.20), residues: 756 sheet: -0.46 (0.19), residues: 702 loop : -1.04 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 999 TYR 0.012 0.001 TYR A1155 PHE 0.024 0.001 PHE B 600 TRP 0.016 0.001 TRP C1197 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (28077) covalent geometry : angle 0.49679 / 0.27 (38232) SS BOND : bond 0.00267 / 0.17 ( 63) SS BOND : angle 1.03511 / 0.75 ( 126) hydrogen bonds : bond 0.04148 / 2.79 ( 971) hydrogen bonds : angle 5.22650 / 3.49 ( 2691) *********************** 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 256 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 168 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8993 (mmm) cc_final: 0.8633 (mmm) REVERT: A 295 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8671 (tmm) REVERT: A 372 MET cc_start: 0.8414 (mmm) cc_final: 0.8176 (mmm) REVERT: A 716 SER cc_start: 0.9164 (m) cc_final: 0.8753 (p) REVERT: A 1001 ASN cc_start: 0.9345 (p0) cc_final: 0.8908 (p0) REVERT: A 1054 ASN cc_start: 0.9184 (OUTLIER) cc_final: 0.8819 (m-40) REVERT: A 1197 TRP cc_start: 0.8546 (m100) cc_final: 0.8189 (m100) REVERT: B 56 VAL cc_start: 0.9471 (OUTLIER) cc_final: 0.9161 (m) REVERT: B 78 MET cc_start: 0.8990 (mmm) cc_final: 0.8696 (mmm) REVERT: B 127 ILE cc_start: 0.9436 (mt) cc_final: 0.9221 (mt) REVERT: B 387 ASN cc_start: 0.8390 (t0) cc_final: 0.7664 (t0) REVERT: B 388 ASN cc_start: 0.8950 (m-40) cc_final: 0.8268 (m-40) REVERT: B 394 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8866 (mt) REVERT: B 546 TYR cc_start: 0.5326 (p90) cc_final: 0.4984 (p90) REVERT: B 716 SER cc_start: 0.9293 (m) cc_final: 0.8858 (p) REVERT: B 772 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7464 (m) REVERT: B 900 LEU cc_start: 0.9219 (tp) cc_final: 0.8984 (tt) REVERT: B 917 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7892 (mt-10) REVERT: B 1092 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8503 (t0) REVERT: B 1232 MET cc_start: 0.6934 (tpt) cc_final: 0.6701 (tpt) REVERT: C 78 MET cc_start: 0.8927 (mmm) cc_final: 0.8622 (mmm) REVERT: C 88 ARG cc_start: 0.8025 (mtt90) cc_final: 0.7660 (mtm-85) REVERT: C 716 SER cc_start: 0.9192 (m) cc_final: 0.8797 (p) REVERT: C 1054 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.8863 (m-40) REVERT: C 1092 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8753 (t0) outliers start: 88 outliers final: 53 residues processed: 247 average time/residue: 0.1473 time to fit residues: 62.0425 Evaluate side-chains 207 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 146 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 725 ASN Chi-restraints excluded: chain B residue 738 TYR Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1092 ASN Chi-restraints excluded: chain B residue 1218 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 708 CYS Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 738 TYR Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 1054 ASN Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1092 ASN 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: 0.6980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 261 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 119 optimal weight: 0.0030 chunk 138 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 340 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 426 GLN B1013 ASN B1130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.095797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.074436 restraints weight = 64790.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.076874 restraints weight = 34886.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.078540 restraints weight = 23237.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.079654 restraints weight = 17721.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.080378 restraints weight = 14805.246| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28140 Z= 0.092 Angle : 0.488 11.698 38358 Z= 0.256 Chirality : 0.042 0.236 4320 Planarity : 0.003 0.041 4938 Dihedral : 4.979 58.781 3848 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.41 % Allowed : 13.60 % Favored : 83.99 % 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: -0.33 (0.14), residues: 3489 helix: 1.80 (0.20), residues: 768 sheet: -0.39 (0.19), residues: 702 loop : -0.97 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 201 TYR 0.010 0.001 TYR A 971 PHE 0.022 0.001 PHE B 600 TRP 0.019 0.001 TRP B1197 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (28077) covalent geometry : angle 0.48539 / 0.26 (38232) SS BOND : bond 0.00336 / 0.17 ( 63) SS BOND : angle 0.97862 / 0.74 ( 126) hydrogen bonds : bond 0.03864 / 2.59 ( 971) hydrogen bonds : angle 5.04346 / 3.37 ( 2691) *********************** 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 248 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 174 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8980 (mmm) cc_final: 0.8647 (mmm) REVERT: A 295 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8359 (tmm) REVERT: A 372 MET cc_start: 0.8358 (mmm) cc_final: 0.8132 (mmm) REVERT: A 716 SER cc_start: 0.9154 (m) cc_final: 0.8691 (p) REVERT: A 1001 ASN cc_start: 0.9327 (p0) cc_final: 0.8840 (p0) REVERT: A 1054 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8809 (m-40) REVERT: A 1197 TRP cc_start: 0.8519 (m100) cc_final: 0.8088 (m100) REVERT: B 78 MET cc_start: 0.8955 (mmm) cc_final: 0.8663 (mmm) REVERT: B 127 ILE cc_start: 0.9392 (mt) cc_final: 0.9172 (mt) REVERT: B 716 SER cc_start: 0.9310 (m) cc_final: 0.8826 (p) REVERT: B 900 LEU cc_start: 0.9202 (tp) cc_final: 0.8975 (tt) REVERT: B 917 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7878 (mt-10) REVERT: B 1092 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8367 (t0) REVERT: B 1232 MET cc_start: 0.6902 (tpt) cc_final: 0.6689 (tpt) REVERT: C 78 MET cc_start: 0.8910 (mmm) cc_final: 0.8599 (mmm) REVERT: C 88 ARG cc_start: 0.7989 (mtt90) cc_final: 0.7639 (mtm-85) REVERT: C 234 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8755 (p) REVERT: C 716 SER cc_start: 0.9071 (m) cc_final: 0.8676 (p) REVERT: C 1054 ASN cc_start: 0.9222 (OUTLIER) cc_final: 0.8876 (m-40) REVERT: C 1092 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8842 (t0) REVERT: C 1120 MET cc_start: 0.8492 (mtm) cc_final: 0.8229 (mtm) REVERT: C 1198 MET cc_start: 0.4367 (mmm) cc_final: 0.4130 (mmm) outliers start: 74 outliers final: 52 residues processed: 241 average time/residue: 0.1451 time to fit residues: 60.2732 Evaluate side-chains 209 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 151 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1092 ASN Chi-restraints excluded: chain B residue 1218 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 708 CYS Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 738 TYR Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 1054 ASN Chi-restraints excluded: chain C residue 1092 ASN Chi-restraints excluded: chain C residue 1111 LEU 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: 0.4980 chunk 224 optimal weight: 9.9990 chunk 285 optimal weight: 8.9990 chunk 347 optimal weight: 8.9990 chunk 311 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 255 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 426 GLN B 995 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.095679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.074393 restraints weight = 64826.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.076835 restraints weight = 34879.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.078491 restraints weight = 23155.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.079600 restraints weight = 17628.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.080287 restraints weight = 14724.006| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28140 Z= 0.100 Angle : 0.490 8.007 38358 Z= 0.257 Chirality : 0.042 0.225 4320 Planarity : 0.003 0.042 4938 Dihedral : 4.875 58.309 3842 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.45 % Allowed : 14.09 % Favored : 83.46 % 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: -0.27 (0.15), residues: 3489 helix: 1.84 (0.20), residues: 774 sheet: -0.48 (0.19), residues: 726 loop : -0.88 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1181 TYR 0.016 0.001 TYR C 166 PHE 0.034 0.001 PHE C 600 TRP 0.019 0.001 TRP C1197 HIS 0.004 0.000 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (28077) covalent geometry : angle 0.48777 / 0.26 (38232) SS BOND : bond 0.00240 / 0.15 ( 63) SS BOND : angle 0.95806 / 0.71 ( 126) hydrogen bonds : bond 0.03805 / 2.56 ( 971) hydrogen bonds : angle 4.95664 / 3.32 ( 2691) *********************** 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 239 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 164 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9000 (mmm) cc_final: 0.8660 (mmm) REVERT: A 295 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8357 (tmm) REVERT: A 546 TYR cc_start: 0.6648 (p90) cc_final: 0.6409 (p90) REVERT: A 716 SER cc_start: 0.9059 (m) cc_final: 0.8649 (p) REVERT: A 1001 ASN cc_start: 0.9327 (p0) cc_final: 0.8837 (p0) REVERT: A 1054 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.8795 (m-40) REVERT: A 1197 TRP cc_start: 0.8496 (m100) cc_final: 0.8034 (m100) REVERT: A 1198 MET cc_start: 0.4550 (mmm) cc_final: 0.4323 (mmm) REVERT: B 78 MET cc_start: 0.8943 (mmm) cc_final: 0.8673 (mmm) REVERT: B 127 ILE cc_start: 0.9393 (mt) cc_final: 0.9191 (mt) REVERT: B 164 CYS cc_start: 0.4169 (m) cc_final: 0.3896 (m) REVERT: B 295 MET cc_start: 0.8799 (ttp) cc_final: 0.8587 (ttp) REVERT: B 388 ASN cc_start: 0.8911 (m-40) cc_final: 0.8343 (m110) REVERT: B 394 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8923 (mt) REVERT: B 409 ILE cc_start: 0.9508 (OUTLIER) cc_final: 0.9285 (mt) REVERT: B 716 SER cc_start: 0.9309 (m) cc_final: 0.8819 (p) REVERT: B 900 LEU cc_start: 0.9230 (tp) cc_final: 0.9023 (tt) REVERT: B 917 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7908 (mt-10) REVERT: B 1092 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8416 (t0) REVERT: C 78 MET cc_start: 0.8902 (mmm) cc_final: 0.8606 (mmm) REVERT: C 88 ARG cc_start: 0.8018 (mtt90) cc_final: 0.7667 (mtm-85) REVERT: C 234 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8801 (p) REVERT: C 716 SER cc_start: 0.8947 (m) cc_final: 0.8640 (p) REVERT: C 840 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8654 (tp40) REVERT: C 1054 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8875 (m-40) REVERT: C 1092 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8814 (t0) REVERT: C 1120 MET cc_start: 0.8563 (mtm) cc_final: 0.8293 (mtm) outliers start: 75 outliers final: 55 residues processed: 232 average time/residue: 0.1436 time to fit residues: 57.1181 Evaluate side-chains 216 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 153 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 725 ASN Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1092 ASN Chi-restraints excluded: chain B residue 1218 MET Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 708 CYS Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 738 TYR Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 1054 ASN Chi-restraints excluded: chain C residue 1092 ASN 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: 7.9990 chunk 330 optimal weight: 5.9990 chunk 267 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 162 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 263 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 256 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.096474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.075205 restraints weight = 64651.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.077652 restraints weight = 34778.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.079312 restraints weight = 23103.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.080428 restraints weight = 17574.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.081155 restraints weight = 14694.560| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28140 Z= 0.088 Angle : 0.485 9.649 38358 Z= 0.252 Chirality : 0.041 0.217 4320 Planarity : 0.003 0.042 4938 Dihedral : 4.757 57.364 3841 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.25 % Allowed : 14.35 % Favored : 83.40 % 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: -0.21 (0.15), residues: 3489 helix: 1.89 (0.20), residues: 774 sheet: -0.40 (0.19), residues: 720 loop : -0.86 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1181 TYR 0.010 0.001 TYR A1155 PHE 0.033 0.001 PHE C 600 TRP 0.018 0.001 TRP C1197 HIS 0.004 0.000 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 (28077) covalent geometry : angle 0.48259 / 0.25 (38232) SS BOND : bond 0.00221 / 0.14 ( 63) SS BOND : angle 0.91694 / 0.67 ( 126) hydrogen bonds : bond 0.03691 / 2.49 ( 971) hydrogen bonds : angle 4.85283 / 3.25 ( 2691) *********************** 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 249 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 180 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8971 (mmm) cc_final: 0.8633 (mmm) REVERT: A 160 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6478 (mt-10) REVERT: A 295 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8317 (tmm) REVERT: A 546 TYR cc_start: 0.6624 (p90) cc_final: 0.6411 (p90) REVERT: A 716 SER cc_start: 0.9031 (m) cc_final: 0.8612 (p) REVERT: A 971 TYR cc_start: 0.9065 (m-80) cc_final: 0.8831 (m-80) REVERT: A 1001 ASN cc_start: 0.9324 (p0) cc_final: 0.8821 (p0) REVERT: A 1054 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8800 (m-40) REVERT: A 1197 TRP cc_start: 0.8551 (m100) cc_final: 0.8140 (m100) REVERT: A 1218 MET cc_start: 0.3677 (tpt) cc_final: 0.3467 (tpt) REVERT: B 78 MET cc_start: 0.8909 (mmm) cc_final: 0.8656 (mmm) REVERT: B 127 ILE cc_start: 0.9376 (mt) cc_final: 0.9157 (mt) REVERT: B 295 MET cc_start: 0.8806 (ttp) cc_final: 0.8586 (ttp) REVERT: B 388 ASN cc_start: 0.8892 (m-40) cc_final: 0.8376 (m110) REVERT: B 409 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9272 (mt) REVERT: B 716 SER cc_start: 0.9304 (m) cc_final: 0.8804 (p) REVERT: B 917 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7887 (mt-10) REVERT: B 1092 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8337 (t0) REVERT: B 1136 PHE cc_start: 0.8679 (t80) cc_final: 0.8388 (t80) REVERT: B 1218 MET cc_start: 0.4579 (OUTLIER) cc_final: 0.4201 (ppp) REVERT: C 78 MET cc_start: 0.8861 (mmm) cc_final: 0.8589 (mmm) REVERT: C 88 ARG cc_start: 0.7998 (mtt90) cc_final: 0.7659 (mtm-85) REVERT: C 164 CYS cc_start: 0.3208 (m) cc_final: 0.2821 (m) REVERT: C 234 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8777 (p) REVERT: C 373 SER cc_start: 0.9068 (m) cc_final: 0.8589 (t) REVERT: C 716 SER cc_start: 0.8959 (m) cc_final: 0.8669 (p) REVERT: C 840 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8645 (tp40) REVERT: C 1054 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8833 (m-40) REVERT: C 1092 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8734 (t0) REVERT: C 1120 MET cc_start: 0.8553 (mtm) cc_final: 0.8289 (mtm) REVERT: C 1198 MET cc_start: 0.4260 (mmm) cc_final: 0.4036 (mmm) outliers start: 69 outliers final: 51 residues processed: 241 average time/residue: 0.1439 time to fit residues: 59.4555 Evaluate side-chains 226 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 167 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 725 ASN Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 817 THR Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1092 ASN Chi-restraints excluded: chain B residue 1218 MET Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 708 CYS Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 738 TYR Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 1054 ASN Chi-restraints excluded: chain C residue 1092 ASN 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: 6.9990 chunk 116 optimal weight: 20.0000 chunk 233 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 305 optimal weight: 5.9990 chunk 345 optimal weight: 6.9990 chunk 328 optimal weight: 8.9990 chunk 261 optimal weight: 0.9980 chunk 262 optimal weight: 0.2980 chunk 58 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.094230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.072841 restraints weight = 65389.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.075228 restraints weight = 35536.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.076864 restraints weight = 23756.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.077942 restraints weight = 18172.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.078647 restraints weight = 15233.735| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28140 Z= 0.159 Angle : 0.534 10.119 38358 Z= 0.277 Chirality : 0.043 0.232 4320 Planarity : 0.003 0.042 4938 Dihedral : 4.894 59.030 3837 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.12 % Allowed : 14.64 % Favored : 83.24 % 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: -0.23 (0.15), residues: 3489 helix: 1.89 (0.20), residues: 762 sheet: -0.45 (0.19), residues: 723 loop : -0.85 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 687 TYR 0.012 0.001 TYR A 442 PHE 0.032 0.001 PHE C 600 TRP 0.017 0.001 TRP C1197 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (28077) covalent geometry : angle 0.53210 / 0.28 (38232) SS BOND : bond 0.00234 / 0.15 ( 63) SS BOND : angle 1.00446 / 0.74 ( 126) hydrogen bonds : bond 0.04010 / 2.70 ( 971) hydrogen bonds : angle 4.96145 / 3.33 ( 2691) ********************** 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 225 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 160 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9036 (mmm) cc_final: 0.8700 (mmm) REVERT: A 160 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6598 (mt-10) REVERT: A 295 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8350 (tmm) REVERT: A 546 TYR cc_start: 0.6708 (p90) cc_final: 0.6489 (p90) REVERT: A 716 SER cc_start: 0.9070 (m) cc_final: 0.8697 (p) REVERT: A 1001 ASN cc_start: 0.9390 (p0) cc_final: 0.8909 (p0) REVERT: A 1054 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8860 (m-40) REVERT: A 1197 TRP cc_start: 0.8511 (m100) cc_final: 0.8144 (m100) REVERT: A 1218 MET cc_start: 0.3785 (tpt) cc_final: 0.3561 (tpt) REVERT: B 78 MET cc_start: 0.8986 (mmm) cc_final: 0.8703 (mmm) REVERT: B 164 CYS cc_start: 0.4184 (m) cc_final: 0.3914 (m) REVERT: B 388 ASN cc_start: 0.8903 (m-40) cc_final: 0.8409 (m110) REVERT: B 394 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8967 (mt) REVERT: B 716 SER cc_start: 0.9327 (m) cc_final: 0.8829 (p) REVERT: B 917 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7900 (mt-10) REVERT: B 1092 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8493 (t0) REVERT: B 1218 MET cc_start: 0.4714 (OUTLIER) cc_final: 0.4273 (ppp) REVERT: C 78 MET cc_start: 0.8965 (mmm) cc_final: 0.8672 (mmm) REVERT: C 88 ARG cc_start: 0.7996 (mtt90) cc_final: 0.7632 (mtm-85) REVERT: C 164 CYS cc_start: 0.3232 (m) cc_final: 0.2835 (m) REVERT: C 234 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8808 (p) REVERT: C 397 MET cc_start: 0.7916 (mtm) cc_final: 0.7643 (mtm) REVERT: C 716 SER cc_start: 0.8963 (m) cc_final: 0.8701 (p) REVERT: C 1054 ASN cc_start: 0.9251 (OUTLIER) cc_final: 0.8865 (m-40) REVERT: C 1092 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8773 (t0) outliers start: 65 outliers final: 52 residues processed: 218 average time/residue: 0.1467 time to fit residues: 55.3536 Evaluate side-chains 211 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 151 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 725 ASN Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 979 SER Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain B residue 1092 ASN Chi-restraints excluded: chain B residue 1218 MET Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 708 CYS Chi-restraints excluded: chain C residue 738 TYR Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 979 SER Chi-restraints excluded: chain C residue 1054 ASN Chi-restraints excluded: chain C residue 1092 ASN 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: 1.9990 chunk 104 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 57 optimal weight: 0.9980 chunk 340 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 315 optimal weight: 0.6980 chunk 257 optimal weight: 10.0000 chunk 297 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.096495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.075184 restraints weight = 64496.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.077627 restraints weight = 34884.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.079303 restraints weight = 23180.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.080423 restraints weight = 17626.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.081048 restraints weight = 14700.023| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2980 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= 0.092 Angle : 0.494 10.273 38358 Z= 0.254 Chirality : 0.042 0.214 4320 Planarity : 0.003 0.042 4938 Dihedral : 4.700 56.486 3837 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.92 % Allowed : 14.81 % Favored : 83.27 % 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: -0.17 (0.15), residues: 3489 helix: 1.95 (0.20), residues: 774 sheet: -0.41 (0.19), residues: 720 loop : -0.83 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 687 TYR 0.011 0.001 TYR A1155 PHE 0.032 0.001 PHE C 600 TRP 0.018 0.001 TRP C1197 HIS 0.004 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (28077) covalent geometry : angle 0.49236 / 0.25 (38232) SS BOND : bond 0.00205 / 0.13 ( 63) SS BOND : angle 0.90089 / 0.66 ( 126) hydrogen bonds : bond 0.03717 / 2.50 ( 971) hydrogen bonds : angle 4.83824 / 3.24 ( 2691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3736.68 seconds wall clock time: 65 minutes 37.40 seconds (3937.40 seconds total)