Starting phenix.real_space_refine on Wed Oct 28 12:12:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y54_72507/10_2026/9y54_72507.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y54_72507/10_2026/9y54_72507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y54_72507/10_2026/9y54_72507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y54_72507/10_2026/9y54_72507.map" model { file = "/net/cci-nas-00/data/ceres_data/9y54_72507/10_2026/9y54_72507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y54_72507/10_2026/9y54_72507.cif" } resolution = 4.55 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= 0.004 sd= 0.046 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 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27450 Number of models: 1 Model: "" Number of chains: 1 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 Restraints were copied for chains: B, C Time building chain proxies: 11.45, per 1000 atoms: 0.42 Number of scatterers: 27450 At special positions: 0 Unit cell: (148.96, 152.76, 163.4, 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 614 " distance=2.03 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 499 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 548 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 578 " distance=2.03 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 597 " distance=2.03 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: 2.14 Conformation dependent library (CDL) restraints added in 1.3 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: 81 helices and 75 sheets defined 25.2% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 344 through 350 removed outlier: 3.696A pdb=" N TRP A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 360 removed outlier: 3.899A pdb=" N TRP A 360 " --> pdb=" O PRO A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 371 through 379 removed outlier: 3.659A pdb=" N LEU A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 removed outlier: 3.657A pdb=" N LYS A 393 " --> pdb=" O ASP A 390 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 394 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR A 395 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY A 396 " --> pdb=" O LYS A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 396' Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.775A pdb=" N PHE A 464 " --> pdb=" O TRP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 707 through 716 Processing helix chain 'A' and resid 825 through 831 Processing helix chain 'A' and resid 834 through 841 Processing helix chain 'A' and resid 844 through 874 removed outlier: 3.886A pdb=" N CYS A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 885 Processing helix chain 'A' and resid 914 through 923 removed outlier: 4.134A pdb=" N LYS A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 937 removed outlier: 3.562A pdb=" N TYR A 935 " --> pdb=" O PHE A 931 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 954 Processing helix chain 'A' and resid 964 through 978 Processing helix chain 'A' and resid 991 through 1002 Processing helix chain 'A' and resid 1006 through 1011 removed outlier: 3.845A pdb=" N LEU A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1032 removed outlier: 3.926A pdb=" N PHE A1032 " --> pdb=" O ILE A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1059 removed outlier: 3.653A pdb=" N GLN A1059 " --> pdb=" O ASN A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1062 No H-bonds generated for 'chain 'A' and resid 1060 through 1062' Processing helix chain 'A' and resid 1070 through 1078 Processing helix chain 'A' and resid 1079 through 1127 removed outlier: 3.816A pdb=" N ALA A1085 " --> pdb=" O LEU A1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 344 through 350 removed outlier: 3.696A pdb=" N TRP B 348 " --> pdb=" O ASN B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 360 removed outlier: 3.899A pdb=" N TRP B 360 " --> pdb=" O PRO B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 357 through 360' Processing helix chain 'B' and resid 371 through 379 removed outlier: 3.658A pdb=" N LEU B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 396 removed outlier: 3.657A pdb=" N LYS B 393 " --> pdb=" O ASP B 390 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE B 394 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TYR B 395 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 396 " --> pdb=" O LYS B 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 390 through 396' Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 458 through 464 removed outlier: 3.775A pdb=" N PHE B 464 " --> pdb=" O TRP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 707 through 716 Processing helix chain 'B' and resid 825 through 831 Processing helix chain 'B' and resid 834 through 841 Processing helix chain 'B' and resid 844 through 874 removed outlier: 3.885A pdb=" N CYS B 848 " --> pdb=" O TYR B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 885 Processing helix chain 'B' and resid 914 through 923 removed outlier: 4.134A pdb=" N LYS B 923 " --> pdb=" O LEU B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 937 removed outlier: 3.561A pdb=" N TYR B 935 " --> pdb=" O PHE B 931 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) 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: 3.845A pdb=" N LEU B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1032 removed outlier: 3.926A pdb=" N PHE B1032 " --> pdb=" O ILE B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1059 removed outlier: 3.652A pdb=" N GLN B1059 " --> pdb=" O ASN B1055 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1062 No H-bonds generated for 'chain 'B' and resid 1060 through 1062' Processing helix chain 'B' and resid 1070 through 1078 Processing helix chain 'B' and resid 1079 through 1127 removed outlier: 3.816A pdb=" N ALA B1085 " --> pdb=" O LEU B1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 92 Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 293 through 303 Processing helix chain 'C' and resid 344 through 350 removed outlier: 3.696A pdb=" N TRP C 348 " --> pdb=" O ASN C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 360 removed outlier: 3.900A pdb=" N TRP C 360 " --> pdb=" O PRO C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 357 through 360' Processing helix chain 'C' and resid 371 through 379 removed outlier: 3.659A pdb=" N LEU C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 396 removed outlier: 3.658A pdb=" N LYS C 393 " --> pdb=" O ASP C 390 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE C 394 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TYR C 395 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 396 " --> pdb=" O LYS C 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 390 through 396' Processing helix chain 'C' and resid 424 through 429 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 458 through 464 removed outlier: 3.775A 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 707 through 716 Processing helix chain 'C' and resid 825 through 831 Processing helix chain 'C' and resid 834 through 841 Processing helix chain 'C' and resid 844 through 874 removed outlier: 3.886A pdb=" N CYS C 848 " --> pdb=" O TYR C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 885 Processing helix chain 'C' and resid 914 through 923 removed outlier: 4.135A pdb=" N LYS C 923 " --> pdb=" O LEU C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 937 removed outlier: 3.561A pdb=" N TYR C 935 " --> pdb=" O PHE C 931 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 937 " --> pdb=" O GLU C 933 " (cutoff:3.500A) 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: 3.846A pdb=" N LEU C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1032 removed outlier: 3.926A pdb=" N PHE C1032 " --> pdb=" O ILE C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1059 removed outlier: 3.651A pdb=" N GLN C1059 " --> pdb=" O ASN C1055 " (cutoff:3.500A) Processing helix chain 'C' and resid 1060 through 1062 No H-bonds generated for 'chain 'C' and resid 1060 through 1062' Processing helix chain 'C' and resid 1070 through 1078 Processing helix chain 'C' and resid 1079 through 1127 removed outlier: 3.816A 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: 4.950A pdb=" N TYR A 75 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N THR A 74 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 76 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 62 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 50 removed outlier: 7.062A pdb=" N THR A 49 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N PHE A 236 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE A 236 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N PHE A 227 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A 238 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR A 217 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 228 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR A 213 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY A 102 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN A 286 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.775A pdb=" N THR A 174 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.674A pdb=" N SER A 97 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL A 163 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.674A pdb=" N SER A 97 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY A 157 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 205 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 114 removed outlier: 4.246A pdb=" N THR A 110 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 121 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 326 removed outlier: 3.578A pdb=" N GLY A 310 " --> pdb=" O PHE A 692 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 692 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 688 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLY A 316 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLY A 686 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG A 687 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG A 704 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 701 " --> pdb=" O VAL A 735 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 727 " --> pdb=" O VAL A 734 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 332 through 335 removed outlier: 3.539A pdb=" N ARG A 335 " --> pdb=" O ASP A 634 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 642 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 633 " --> pdb=" O GLY A 640 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY A 640 " --> pdb=" O TYR A 633 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 678 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A 669 " --> pdb=" O PHE A 678 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 668 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.642A pdb=" N VAL A 354 " --> pdb=" O SER A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 365 removed outlier: 3.915A pdb=" N GLU A 361 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 406 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS A 606 " --> pdb=" O SER A 401 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 445 " --> pdb=" O CYS A 597 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER A 438 " --> pdb=" O CYS A 386 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N CYS A 386 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN A 440 " --> pdb=" O PHE A 384 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A 384 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR A 442 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 365 removed outlier: 3.915A pdb=" N GLU A 361 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 406 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS A 606 " --> pdb=" O SER A 401 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 596 " --> pdb=" O GLN A 593 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 369 through 370 removed outlier: 3.953A 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 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 498 through 502 removed outlier: 3.692A pdb=" N CYS A 499 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU A 529 " --> pdb=" O CYS A 499 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N CYS A 501 " --> pdb=" O LEU A 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 565 through 566 removed outlier: 3.787A pdb=" N ALA A 565 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 571 through 572 Processing sheet with id=AC1, first strand: chain 'A' and resid 738 through 745 removed outlier: 6.306A pdb=" N PHE A 776 " --> pdb=" O ASN A 739 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR A 741 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASN A 778 " --> pdb=" O THR A 741 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE A 743 " --> pdb=" O ASN A 778 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR A 756 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 752 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 785 through 787 removed outlier: 6.474A pdb=" N ASN A 785 " --> pdb=" O LEU B 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 798 through 803 Processing sheet with id=AC4, first strand: chain 'A' and resid 806 through 816 removed outlier: 3.783A pdb=" N PHE A1159 " --> pdb=" O ILE A1144 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE A1144 " --> pdb=" O PHE A1159 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR A1161 " --> pdb=" O HIS A1142 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N HIS A1142 " --> pdb=" O TYR A1161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 821 through 824 removed outlier: 4.092A pdb=" N LYS A 821 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A 823 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 957 " --> pdb=" O THR A 823 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 878 through 880 Processing sheet with id=AC7, first strand: chain 'A' and resid 1215 through 1218 removed outlier: 3.684A pdb=" N LEU A1175 " --> pdb=" O ILE A1183 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1188 through 1193 removed outlier: 3.772A pdb=" N THR A1200 " --> pdb=" O TYR A1189 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AD1, first strand: chain 'B' and resid 36 through 40 removed outlier: 4.950A pdb=" N TYR B 75 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N THR B 74 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 76 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 62 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 49 through 50 removed outlier: 7.062A pdb=" N THR B 49 " --> pdb=" O THR B 234 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N PHE B 236 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N PHE B 236 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE B 227 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE B 238 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR B 217 " --> pdb=" O TYR B 224 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR B 228 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR B 213 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY B 102 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN B 286 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.775A pdb=" N THR B 174 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.674A pdb=" N SER B 97 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B 163 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.674A pdb=" N SER B 97 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY B 157 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR B 205 " --> pdb=" O GLY B 157 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 110 through 114 removed outlier: 4.246A pdb=" N THR B 110 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 121 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 310 through 326 removed outlier: 3.578A pdb=" N GLY B 310 " --> pdb=" O PHE B 692 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 692 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B 688 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY B 316 " --> pdb=" O GLY B 686 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLY B 686 " --> pdb=" O GLY B 316 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG B 687 " --> pdb=" O ARG B 704 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ARG B 704 " --> pdb=" O ARG B 687 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 701 " --> pdb=" O VAL B 735 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 727 " --> pdb=" O VAL B 734 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 332 through 335 removed outlier: 3.539A pdb=" N ARG B 335 " --> pdb=" O ASP B 634 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 642 " --> pdb=" O VAL B 631 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR B 633 " --> pdb=" O GLY B 640 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY B 640 " --> pdb=" O TYR B 633 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 678 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE B 669 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 3.637A 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: 6.642A pdb=" N VAL B 354 " --> pdb=" O SER B 453 " (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: 3.916A pdb=" N GLU B 361 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS B 406 " --> pdb=" O GLU B 361 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS B 606 " --> pdb=" O SER B 401 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 445 " --> pdb=" O CYS B 597 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER B 438 " --> pdb=" O CYS B 386 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N CYS B 386 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN B 440 " --> pdb=" O PHE B 384 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE B 384 " --> pdb=" O GLN B 440 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR B 442 " --> pdb=" O ASP B 382 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.916A pdb=" N GLU B 361 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS B 406 " --> pdb=" O GLU B 361 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS B 606 " --> pdb=" O SER B 401 " (cutoff:3.500A) removed outlier: 3.790A 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: 3.953A pdb=" N PHE B 370 " --> pdb=" O CYS B 614 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 484 through 488 Processing sheet with id=AE5, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AE6, first strand: chain 'B' and resid 498 through 502 removed outlier: 3.693A pdb=" N CYS B 499 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU B 529 " --> pdb=" O CYS B 499 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N CYS B 501 " --> pdb=" O LEU B 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'B' and resid 565 through 566 removed outlier: 3.786A pdb=" N ALA B 565 " --> pdb=" O LEU B 584 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 571 through 572 Processing sheet with id=AE9, first strand: chain 'B' and resid 738 through 745 removed outlier: 6.306A pdb=" N PHE B 776 " --> pdb=" O ASN B 739 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR B 741 " --> pdb=" O PHE B 776 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASN B 778 " --> pdb=" O THR B 741 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 743 " --> pdb=" O ASN B 778 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR B 756 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 752 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 785 through 787 removed outlier: 5.704A pdb=" N ASN B 785 " --> pdb=" O LEU C 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'B' and resid 798 through 803 Processing sheet with id=AF3, first strand: chain 'B' and resid 806 through 816 removed outlier: 3.783A pdb=" N PHE B1159 " --> pdb=" O ILE B1144 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE B1144 " --> pdb=" O PHE B1159 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR B1161 " --> pdb=" O HIS B1142 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N HIS B1142 " --> pdb=" O TYR B1161 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 821 through 824 removed outlier: 4.093A pdb=" N LYS B 821 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR B 823 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 957 " --> pdb=" O THR B 823 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 1215 through 1218 removed outlier: 3.685A pdb=" N LEU B1175 " --> pdb=" O ILE B1183 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 1188 through 1193 removed outlier: 3.772A pdb=" N THR B1200 " --> pdb=" O TYR B1189 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AF8, first strand: chain 'C' and resid 36 through 40 removed outlier: 4.950A pdb=" N TYR C 75 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N THR C 74 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG C 76 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 62 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 49 through 50 removed outlier: 7.062A pdb=" N THR C 49 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N PHE C 236 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE C 236 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N PHE C 227 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE C 238 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR C 217 " --> pdb=" O TYR C 224 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR C 228 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR C 213 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY C 102 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.395A 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: 6.774A 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: 3.674A pdb=" N SER C 97 " --> pdb=" O TYR C 249 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL C 163 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.674A pdb=" N SER C 97 " --> pdb=" O TYR C 249 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY C 157 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR C 205 " --> pdb=" O GLY C 157 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 110 through 114 removed outlier: 4.245A pdb=" N THR C 110 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU C 121 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 310 through 326 removed outlier: 3.578A pdb=" N GLY C 310 " --> pdb=" O PHE C 692 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 692 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL C 688 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY C 316 " --> pdb=" O GLY C 686 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLY C 686 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ARG C 687 " --> pdb=" O ARG C 704 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ARG C 704 " --> pdb=" O ARG C 687 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 701 " --> pdb=" O VAL C 735 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 727 " --> pdb=" O VAL C 734 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 332 through 335 removed outlier: 3.539A pdb=" N ARG C 335 " --> pdb=" O ASP C 634 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C 642 " --> pdb=" O VAL C 631 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR C 633 " --> pdb=" O GLY C 640 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY C 640 " --> pdb=" O TYR C 633 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 678 " --> pdb=" O PHE C 669 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE C 669 " --> pdb=" O PHE C 678 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR C 667 " --> pdb=" O ILE C 680 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 668 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 353 through 355 removed outlier: 6.642A pdb=" N VAL C 354 " --> pdb=" O SER C 453 " (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: 3.915A pdb=" N GLU C 361 " --> pdb=" O LYS C 406 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS C 406 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER C 401 " --> pdb=" O HIS C 606 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS C 606 " --> pdb=" O SER C 401 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C 445 " --> pdb=" O CYS C 597 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N SER C 438 " --> pdb=" O CYS C 386 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N CYS C 386 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN C 440 " --> pdb=" O PHE C 384 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE C 384 " --> pdb=" O GLN C 440 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR C 442 " --> pdb=" O ASP C 382 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 361 through 365 removed outlier: 3.915A pdb=" N GLU C 361 " --> pdb=" O LYS C 406 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS C 406 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER C 401 " --> pdb=" O HIS C 606 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS C 606 " --> pdb=" O SER C 401 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS C 596 " --> pdb=" O GLN C 593 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 369 through 370 removed outlier: 3.953A pdb=" N PHE C 370 " --> pdb=" O CYS C 614 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 484 through 488 Processing sheet with id=AH3, first strand: chain 'C' and resid 492 through 493 Processing sheet with id=AH4, first strand: chain 'C' and resid 498 through 502 removed outlier: 3.693A pdb=" N CYS C 499 " --> pdb=" O ASN C 527 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU C 529 " --> pdb=" O CYS C 499 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N CYS C 501 " --> pdb=" O LEU C 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'C' and resid 565 through 566 removed outlier: 3.786A pdb=" N ALA C 565 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 571 through 572 Processing sheet with id=AH7, first strand: chain 'C' and resid 738 through 745 removed outlier: 6.305A pdb=" N PHE C 776 " --> pdb=" O ASN C 739 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR C 741 " --> pdb=" O PHE C 776 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN C 778 " --> pdb=" O THR C 741 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 743 " --> pdb=" O ASN C 778 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR C 756 " --> pdb=" O VAL C 752 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 752 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 798 through 803 Processing sheet with id=AH9, first strand: chain 'C' and resid 806 through 816 removed outlier: 3.783A pdb=" N PHE C1159 " --> pdb=" O ILE C1144 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE C1144 " --> pdb=" O PHE C1159 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR C1161 " --> pdb=" O HIS C1142 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N HIS C1142 " --> pdb=" O TYR C1161 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 821 through 824 removed outlier: 4.093A pdb=" N LYS C 821 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 823 " --> pdb=" O LYS C 957 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 957 " --> pdb=" O THR C 823 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 1215 through 1218 removed outlier: 3.685A pdb=" N LEU C1175 " --> pdb=" O ILE C1183 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 1188 through 1193 removed outlier: 3.774A pdb=" N THR C1200 " --> pdb=" O TYR C1189 " (cutoff:3.500A) 1067 hydrogen bonds defined for protein. 2976 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: 7.12 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8835 1.35 - 1.47: 7029 1.47 - 1.59: 11976 1.59 - 1.71: 0 1.71 - 1.83: 237 Bond restraints: 28077 Sorted by residual: bond pdb=" N TYR A1152 " pdb=" CA TYR A1152 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.39e-02 5.18e+03 7.60e-01 bond pdb=" N TYR B1152 " pdb=" CA TYR B1152 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.39e-02 5.18e+03 7.53e-01 bond pdb=" N TYR C1152 " pdb=" CA TYR C1152 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.39e-02 5.18e+03 7.10e-01 bond pdb=" CA SER A 897 " pdb=" C SER A 897 " ideal model delta sigma weight residual 1.525 1.535 -0.010 1.19e-02 7.06e+03 7.04e-01 bond pdb=" C VAL A 479 " pdb=" O VAL A 479 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 6.84e-01 ... (remaining 28072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 37451 1.50 - 3.00: 708 3.00 - 4.49: 63 4.49 - 5.99: 7 5.99 - 7.49: 3 Bond angle restraints: 38232 Sorted by residual: angle pdb=" C ASN B 387 " pdb=" N ASN B 388 " pdb=" CA ASN B 388 " ideal model delta sigma weight residual 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C ASN C 387 " pdb=" N ASN C 388 " pdb=" CA ASN C 388 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.53e+01 angle pdb=" C ASN A 387 " pdb=" N ASN A 388 " pdb=" CA ASN A 388 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" N VAL A1009 " pdb=" CA VAL A1009 " pdb=" C VAL A1009 " ideal model delta sigma weight residual 111.58 107.76 3.82 1.06e+00 8.90e-01 1.30e+01 angle pdb=" N VAL C1009 " pdb=" CA VAL C1009 " pdb=" C VAL C1009 " ideal model delta sigma weight residual 111.58 107.78 3.80 1.06e+00 8.90e-01 1.29e+01 ... (remaining 38227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.82: 15290 13.82 - 27.65: 1088 27.65 - 41.47: 245 41.47 - 55.29: 75 55.29 - 69.11: 36 Dihedral angle restraints: 16734 sinusoidal: 6429 harmonic: 10305 Sorted by residual: dihedral pdb=" CB CYS B 491 " pdb=" SG CYS B 491 " pdb=" SG CYS B 561 " pdb=" CB CYS B 561 " ideal model delta sinusoidal sigma weight residual -86.00 -121.36 35.36 1 1.00e+01 1.00e-02 1.77e+01 dihedral pdb=" CB CYS A 491 " pdb=" SG CYS A 491 " pdb=" SG CYS A 561 " pdb=" CB CYS A 561 " ideal model delta sinusoidal sigma weight residual -86.00 -121.34 35.34 1 1.00e+01 1.00e-02 1.77e+01 dihedral pdb=" CB CYS C 491 " pdb=" SG CYS C 491 " pdb=" SG CYS C 561 " pdb=" CB CYS C 561 " ideal model delta sinusoidal sigma weight residual -86.00 -121.34 35.34 1 1.00e+01 1.00e-02 1.77e+01 ... (remaining 16731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2772 0.029 - 0.059: 853 0.059 - 0.088: 389 0.088 - 0.118: 253 0.118 - 0.147: 53 Chirality restraints: 4320 Sorted by residual: chirality pdb=" CA ILE B 802 " pdb=" N ILE B 802 " pdb=" C ILE B 802 " pdb=" CB ILE B 802 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE C 802 " pdb=" N ILE C 802 " pdb=" C ILE C 802 " pdb=" CB ILE C 802 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILE A 802 " pdb=" N ILE A 802 " pdb=" C ILE A 802 " pdb=" CB ILE A 802 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 4317 not shown) Planarity restraints: 4938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 897 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO A 898 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 898 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 898 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 897 " 0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO B 898 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 898 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 898 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 897 " -0.046 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO C 898 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 898 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 898 " -0.039 5.00e-02 4.00e+02 ... (remaining 4935 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6706 2.79 - 3.32: 22715 3.32 - 3.84: 46338 3.84 - 4.37: 51311 4.37 - 4.90: 87924 Nonbonded interactions: 214994 Sorted by model distance: nonbonded pdb=" OH TYR A 971 " pdb=" OE2 GLU C 780 " model vdw 2.261 3.040 nonbonded pdb=" O GLN C 868 " pdb=" OG SER C 872 " model vdw 2.282 3.040 nonbonded pdb=" O GLN B 868 " pdb=" OG SER B 872 " model vdw 2.282 3.040 nonbonded pdb=" O GLN A 868 " pdb=" OG SER A 872 " model vdw 2.282 3.040 nonbonded pdb=" O PRO C 898 " pdb=" OG SER C 914 " model vdw 2.302 3.040 ... (remaining 214989 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. 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: 5.350 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: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 32.270 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.002 0.035 28140 Z= 0.127 Angle : 0.520 7.490 38358 Z= 0.310 Chirality : 0.042 0.147 4320 Planarity : 0.005 0.069 4938 Dihedral : 10.921 69.113 9957 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.31 % Allowed : 5.87 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.13), residues: 3489 helix: -0.31 (0.17), residues: 693 sheet: 0.04 (0.19), residues: 714 loop : -1.39 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 362 TYR 0.011 0.001 TYR B 667 PHE 0.012 0.001 PHE B 407 TRP 0.009 0.001 TRP B 348 HIS 0.003 0.001 HIS C 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (28077) covalent geometry : angle 0.51945 / 0.31 (38232) SS BOND : bond 0.00208 / 0.14 ( 63) SS BOND : angle 0.72082 / 0.50 ( 126) hydrogen bonds : bond 0.23581 / 15.38 ( 980) hydrogen bonds : angle 7.87661 / 5.34 ( 2976) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 203 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.9755 (tp) cc_final: 0.9415 (tp) REVERT: A 64 LEU cc_start: 0.9666 (mt) cc_final: 0.9272 (mp) REVERT: A 78 MET cc_start: 0.9182 (mmm) cc_final: 0.8666 (mmm) REVERT: A 120 SER cc_start: 0.9339 (p) cc_final: 0.8966 (t) REVERT: A 159 LEU cc_start: 0.9369 (mt) cc_final: 0.9147 (mt) REVERT: A 246 LEU cc_start: 0.9242 (mt) cc_final: 0.8921 (mp) REVERT: A 326 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.9028 (m) REVERT: A 356 SER cc_start: 0.9668 (m) cc_final: 0.9303 (t) REVERT: A 372 MET cc_start: 0.9491 (mmm) cc_final: 0.9138 (tpp) REVERT: A 375 LEU cc_start: 0.9585 (mt) cc_final: 0.9244 (tt) REVERT: A 376 MET cc_start: 0.9366 (mtm) cc_final: 0.8865 (ptt) REVERT: A 421 ASN cc_start: 0.8928 (m110) cc_final: 0.8720 (m110) REVERT: A 469 ASP cc_start: 0.9541 (m-30) cc_final: 0.9319 (t0) REVERT: A 564 LEU cc_start: 0.9366 (mt) cc_final: 0.9101 (mm) REVERT: A 669 PHE cc_start: 0.9602 (p90) cc_final: 0.9325 (p90) REVERT: A 689 SER cc_start: 0.9137 (m) cc_final: 0.8523 (p) REVERT: A 741 THR cc_start: 0.9250 (OUTLIER) cc_final: 0.8989 (m) REVERT: A 859 ASN cc_start: 0.9629 (m-40) cc_final: 0.9354 (m-40) REVERT: A 872 SER cc_start: 0.9484 (OUTLIER) cc_final: 0.9248 (p) REVERT: A 1025 LEU cc_start: 0.9690 (mt) cc_final: 0.9430 (pp) REVERT: A 1064 PHE cc_start: 0.8133 (m-80) cc_final: 0.7810 (m-80) REVERT: A 1078 LEU cc_start: 0.8298 (mt) cc_final: 0.7775 (tp) REVERT: A 1104 GLN cc_start: 0.9195 (mt0) cc_final: 0.8476 (tm-30) REVERT: A 1107 SER cc_start: 0.9613 (m) cc_final: 0.9326 (p) REVERT: A 1108 ASP cc_start: 0.9086 (m-30) cc_final: 0.8581 (m-30) REVERT: A 1120 MET cc_start: 0.9093 (mtm) cc_final: 0.8639 (mmm) REVERT: A 1121 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8307 (mt-10) REVERT: A 1233 LEU cc_start: 0.6711 (tp) cc_final: 0.6340 (pt) outliers start: 44 outliers final: 13 residues processed: 237 average time/residue: 0.0602 time to fit residues: 21.3605 Evaluate side-chains 133 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 HIS A 429 ASN ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.053356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.040686 restraints weight = 47883.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.042303 restraints weight = 27187.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.043452 restraints weight = 18055.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.044313 restraints weight = 13296.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.044903 restraints weight = 10455.381| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 28140 Z= 0.156 Angle : 0.626 11.206 38358 Z= 0.338 Chirality : 0.044 0.211 4320 Planarity : 0.005 0.060 4938 Dihedral : 4.415 24.413 3819 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.29 % Allowed : 2.94 % Favored : 96.77 % 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: -0.51 (0.14), residues: 3489 helix: 1.00 (0.19), residues: 726 sheet: 0.16 (0.19), residues: 723 loop : -1.04 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 945 TYR 0.033 0.002 TYR C 971 PHE 0.027 0.002 PHE C1021 TRP 0.012 0.001 TRP C 188 HIS 0.009 0.001 HIS A 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (28077) covalent geometry : angle 0.60747 / 0.33 (38232) SS BOND : bond 0.00467 / 0.30 ( 63) SS BOND : angle 2.68437 / 1.92 ( 126) hydrogen bonds : bond 0.04848 / 3.20 ( 980) hydrogen bonds : angle 5.84216 / 3.97 ( 2976) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 0.337 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: C 64 LEU cc_start: 0.9585 (mt) cc_final: 0.9234 (mp) REVERT: C 78 MET cc_start: 0.9097 (mmm) cc_final: 0.8605 (mmm) REVERT: C 250 TYR cc_start: 0.8072 (t80) cc_final: 0.7352 (t80) REVERT: C 313 GLU cc_start: 0.9152 (mp0) cc_final: 0.8838 (tp30) REVERT: C 372 MET cc_start: 0.9445 (mmm) cc_final: 0.8957 (tpp) REVERT: C 375 LEU cc_start: 0.9611 (mt) cc_final: 0.9374 (tt) REVERT: C 376 MET cc_start: 0.9375 (mtm) cc_final: 0.9046 (ppp) REVERT: C 379 ILE cc_start: 0.9383 (mm) cc_final: 0.9084 (mm) REVERT: C 397 MET cc_start: 0.8376 (mtp) cc_final: 0.8007 (mtp) REVERT: C 416 ASP cc_start: 0.9162 (m-30) cc_final: 0.8892 (m-30) REVERT: C 426 GLN cc_start: 0.9024 (mt0) cc_final: 0.8559 (mm-40) REVERT: C 469 ASP cc_start: 0.9492 (m-30) cc_final: 0.9098 (t0) REVERT: C 659 LEU cc_start: 0.9132 (tp) cc_final: 0.8778 (tp) REVERT: C 717 LEU cc_start: 0.9658 (mt) cc_final: 0.9448 (mp) REVERT: C 859 ASN cc_start: 0.9540 (m-40) cc_final: 0.9152 (m-40) REVERT: C 863 ASP cc_start: 0.9358 (m-30) cc_final: 0.9111 (m-30) REVERT: C 959 LEU cc_start: 0.9156 (tp) cc_final: 0.8744 (tp) REVERT: C 971 TYR cc_start: 0.9216 (m-10) cc_final: 0.8899 (m-80) REVERT: C 1062 ASN cc_start: 0.7442 (t0) cc_final: 0.6729 (t0) REVERT: C 1078 LEU cc_start: 0.8269 (mt) cc_final: 0.7848 (tp) REVERT: C 1082 GLU cc_start: 0.9529 (mp0) cc_final: 0.9259 (mp0) REVERT: C 1104 GLN cc_start: 0.9274 (mt0) cc_final: 0.8850 (tm-30) REVERT: C 1120 MET cc_start: 0.9240 (mtm) cc_final: 0.9014 (mtm) REVERT: C 1121 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8430 (mt-10) REVERT: C 1122 LYS cc_start: 0.8922 (mmtp) cc_final: 0.8514 (tppt) outliers start: 3 outliers final: 1 residues processed: 160 average time/residue: 0.0638 time to fit residues: 15.8741 Evaluate side-chains 105 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [248, 218, 61, 87, 131, 350, 99, 118, 306, 160, 92] chunk 248 optimal weight: 8.9990 chunk 218 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 350 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 306 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 189 HIS ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.052557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.039868 restraints weight = 48997.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.041477 restraints weight = 27723.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.042663 restraints weight = 18519.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.043532 restraints weight = 13592.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.044194 restraints weight = 10642.163| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28140 Z= 0.159 Angle : 0.555 7.226 38358 Z= 0.297 Chirality : 0.042 0.178 4320 Planarity : 0.004 0.052 4938 Dihedral : 4.269 17.945 3819 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.10 % Allowed : 3.13 % Favored : 96.77 % 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: -0.38 (0.14), residues: 3489 helix: 1.17 (0.19), residues: 765 sheet: 0.13 (0.19), residues: 705 loop : -0.96 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 681 TYR 0.029 0.001 TYR C 667 PHE 0.021 0.001 PHE B 782 TRP 0.015 0.001 TRP B 348 HIS 0.005 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (28077) covalent geometry : angle 0.54895 / 0.29 (38232) SS BOND : bond 0.00464 / 0.31 ( 63) SS BOND : angle 1.53502 / 1.02 ( 126) hydrogen bonds : bond 0.04108 / 2.70 ( 980) hydrogen bonds : angle 5.39391 / 3.67 ( 2976) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 LEU cc_start: 0.9574 (mt) cc_final: 0.9177 (mp) REVERT: C 78 MET cc_start: 0.9103 (mmm) cc_final: 0.8693 (mmm) REVERT: C 118 MET cc_start: 0.7853 (tpp) cc_final: 0.7408 (tpp) REVERT: C 246 LEU cc_start: 0.9300 (mp) cc_final: 0.9075 (mp) REVERT: C 250 TYR cc_start: 0.8074 (t80) cc_final: 0.7298 (t80) REVERT: C 372 MET cc_start: 0.9472 (mmm) cc_final: 0.8848 (tpp) REVERT: C 375 LEU cc_start: 0.9588 (mt) cc_final: 0.9343 (tt) REVERT: C 376 MET cc_start: 0.9364 (mtm) cc_final: 0.8995 (ppp) REVERT: C 379 ILE cc_start: 0.9388 (mm) cc_final: 0.9079 (mm) REVERT: C 397 MET cc_start: 0.8240 (mtp) cc_final: 0.8009 (mtp) REVERT: C 416 ASP cc_start: 0.9181 (m-30) cc_final: 0.8874 (m-30) REVERT: C 426 GLN cc_start: 0.9072 (mt0) cc_final: 0.8612 (mm-40) REVERT: C 469 ASP cc_start: 0.9513 (m-30) cc_final: 0.9103 (t0) REVERT: C 717 LEU cc_start: 0.9649 (mt) cc_final: 0.9392 (mp) REVERT: C 849 ASP cc_start: 0.9291 (m-30) cc_final: 0.8976 (p0) REVERT: C 852 ASN cc_start: 0.9593 (m-40) cc_final: 0.9266 (m110) REVERT: C 859 ASN cc_start: 0.9568 (m-40) cc_final: 0.9216 (m-40) REVERT: C 873 LEU cc_start: 0.9364 (mm) cc_final: 0.9149 (mm) REVERT: C 959 LEU cc_start: 0.9264 (tp) cc_final: 0.8844 (tp) REVERT: C 1062 ASN cc_start: 0.7921 (t0) cc_final: 0.7024 (t0) REVERT: C 1064 PHE cc_start: 0.8335 (m-80) cc_final: 0.7123 (m-80) REVERT: C 1075 LEU cc_start: 0.9492 (mm) cc_final: 0.9281 (mm) REVERT: C 1078 LEU cc_start: 0.8250 (mt) cc_final: 0.7809 (tp) REVERT: C 1082 GLU cc_start: 0.9557 (mp0) cc_final: 0.9254 (mp0) REVERT: C 1104 GLN cc_start: 0.9161 (mt0) cc_final: 0.8482 (tm-30) REVERT: C 1108 ASP cc_start: 0.9030 (m-30) cc_final: 0.8370 (m-30) REVERT: C 1120 MET cc_start: 0.9310 (mtm) cc_final: 0.9069 (mtm) REVERT: C 1122 LYS cc_start: 0.8918 (mmtp) cc_final: 0.8553 (tppt) REVERT: C 1149 ASN cc_start: 0.9085 (t0) cc_final: 0.8437 (p0) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.0595 time to fit residues: 12.2043 Evaluate side-chains 103 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [155, 105, 149, 75, 80, 140, 183, 54, 73, 188, 348] chunk 155 optimal weight: 0.0000 chunk 105 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 0.0470 chunk 140 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 188 optimal weight: 10.0000 chunk 348 optimal weight: 20.0000 overall best weight: 1.3686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 173 GLN ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.053583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.040697 restraints weight = 48008.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.042334 restraints weight = 27341.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.043557 restraints weight = 18324.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.044453 restraints weight = 13451.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.045015 restraints weight = 10560.804| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28140 Z= 0.105 Angle : 0.507 7.062 38358 Z= 0.271 Chirality : 0.042 0.155 4320 Planarity : 0.004 0.078 4938 Dihedral : 4.130 20.528 3819 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.10 % Allowed : 1.96 % Favored : 97.95 % 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: -0.20 (0.14), residues: 3489 helix: 1.51 (0.19), residues: 747 sheet: 0.20 (0.19), residues: 726 loop : -0.91 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 687 TYR 0.015 0.001 TYR C 667 PHE 0.023 0.001 PHE A 782 TRP 0.012 0.001 TRP C 348 HIS 0.003 0.001 HIS C 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (28077) covalent geometry : angle 0.50280 / 0.27 (38232) SS BOND : bond 0.00275 / 0.19 ( 63) SS BOND : angle 1.29549 / 0.82 ( 126) hydrogen bonds : bond 0.03748 / 2.47 ( 980) hydrogen bonds : angle 5.07997 / 3.45 ( 2976) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 LEU cc_start: 0.9574 (mt) cc_final: 0.9181 (mp) REVERT: C 78 MET cc_start: 0.9114 (mmm) cc_final: 0.8690 (mmm) REVERT: C 118 MET cc_start: 0.7889 (tpp) cc_final: 0.7454 (tpp) REVERT: C 250 TYR cc_start: 0.7945 (t80) cc_final: 0.7220 (t80) REVERT: C 372 MET cc_start: 0.9438 (mmm) cc_final: 0.8826 (tpp) REVERT: C 375 LEU cc_start: 0.9571 (mt) cc_final: 0.9307 (tt) REVERT: C 376 MET cc_start: 0.9347 (mtm) cc_final: 0.8994 (ppp) REVERT: C 379 ILE cc_start: 0.9373 (mm) cc_final: 0.9056 (mm) REVERT: C 387 ASN cc_start: 0.8973 (t0) cc_final: 0.8734 (t0) REVERT: C 416 ASP cc_start: 0.9117 (m-30) cc_final: 0.8819 (m-30) REVERT: C 426 GLN cc_start: 0.9075 (mt0) cc_final: 0.8629 (mm-40) REVERT: C 469 ASP cc_start: 0.9522 (m-30) cc_final: 0.9109 (t0) REVERT: C 717 LEU cc_start: 0.9645 (mt) cc_final: 0.9383 (mp) REVERT: C 825 ASP cc_start: 0.6604 (m-30) cc_final: 0.6362 (p0) REVERT: C 849 ASP cc_start: 0.9264 (m-30) cc_final: 0.8940 (p0) REVERT: C 852 ASN cc_start: 0.9579 (m-40) cc_final: 0.9246 (m110) REVERT: C 859 ASN cc_start: 0.9552 (m-40) cc_final: 0.9313 (m-40) REVERT: C 959 LEU cc_start: 0.9324 (tp) cc_final: 0.8878 (tp) REVERT: C 1021 PHE cc_start: 0.9519 (m-80) cc_final: 0.8876 (m-80) REVERT: C 1062 ASN cc_start: 0.7893 (t0) cc_final: 0.7032 (t0) REVERT: C 1064 PHE cc_start: 0.8292 (m-80) cc_final: 0.7468 (m-80) REVERT: C 1075 LEU cc_start: 0.9479 (mm) cc_final: 0.9266 (mm) REVERT: C 1078 LEU cc_start: 0.8212 (mt) cc_final: 0.7823 (tp) REVERT: C 1082 GLU cc_start: 0.9565 (mp0) cc_final: 0.9200 (mp0) REVERT: C 1104 GLN cc_start: 0.9132 (mt0) cc_final: 0.8431 (tm-30) REVERT: C 1108 ASP cc_start: 0.9020 (m-30) cc_final: 0.8350 (m-30) REVERT: C 1120 MET cc_start: 0.9263 (mtm) cc_final: 0.9058 (mtm) REVERT: C 1122 LYS cc_start: 0.8873 (mmtp) cc_final: 0.8528 (tppt) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.0699 time to fit residues: 13.5311 Evaluate side-chains 103 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [348, 216, 61, 128, 170, 162, 163, 272, 188, 301, 337] chunk 348 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 162 optimal weight: 0.0070 chunk 163 optimal weight: 10.0000 chunk 272 optimal weight: 0.0470 chunk 188 optimal weight: 9.9990 chunk 301 optimal weight: 5.9990 chunk 337 optimal weight: 5.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.054210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.041242 restraints weight = 46680.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.042869 restraints weight = 26874.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.044088 restraints weight = 18206.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.044983 restraints weight = 13428.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.045663 restraints weight = 10562.330| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28140 Z= 0.089 Angle : 0.501 7.529 38358 Z= 0.261 Chirality : 0.042 0.158 4320 Planarity : 0.005 0.119 4938 Dihedral : 3.985 18.586 3819 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -0.07 (0.14), residues: 3489 helix: 1.49 (0.19), residues: 765 sheet: 0.34 (0.19), residues: 720 loop : -0.81 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 687 TYR 0.011 0.001 TYR C 684 PHE 0.016 0.001 PHE C 782 TRP 0.005 0.001 TRP B 348 HIS 0.003 0.001 HIS C 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 (28077) covalent geometry : angle 0.49798 / 0.26 (38232) SS BOND : bond 0.00336 / 0.20 ( 63) SS BOND : angle 1.10487 / 0.70 ( 126) hydrogen bonds : bond 0.03579 / 2.35 ( 980) hydrogen bonds : angle 4.80674 / 3.27 ( 2976) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 LEU cc_start: 0.9584 (mt) cc_final: 0.9160 (mp) REVERT: C 78 MET cc_start: 0.9120 (mmm) cc_final: 0.8700 (mmm) REVERT: C 118 MET cc_start: 0.7870 (tpp) cc_final: 0.7388 (tpp) REVERT: C 250 TYR cc_start: 0.7919 (t80) cc_final: 0.7216 (t80) REVERT: C 372 MET cc_start: 0.9400 (mmm) cc_final: 0.9199 (ttm) REVERT: C 376 MET cc_start: 0.9322 (mtm) cc_final: 0.9032 (ppp) REVERT: C 379 ILE cc_start: 0.9334 (mm) cc_final: 0.8945 (pt) REVERT: C 416 ASP cc_start: 0.9097 (m-30) cc_final: 0.8815 (m-30) REVERT: C 426 GLN cc_start: 0.9083 (mt0) cc_final: 0.8629 (mm-40) REVERT: C 469 ASP cc_start: 0.9523 (m-30) cc_final: 0.9117 (t0) REVERT: C 559 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7357 (mp0) REVERT: C 659 LEU cc_start: 0.8308 (tp) cc_final: 0.8089 (tp) REVERT: C 717 LEU cc_start: 0.9652 (mt) cc_final: 0.9381 (mp) REVERT: C 849 ASP cc_start: 0.9235 (m-30) cc_final: 0.8938 (p0) REVERT: C 852 ASN cc_start: 0.9558 (m-40) cc_final: 0.9245 (m110) REVERT: C 859 ASN cc_start: 0.9527 (m-40) cc_final: 0.9293 (m-40) REVERT: C 865 THR cc_start: 0.9756 (p) cc_final: 0.9434 (p) REVERT: C 868 GLN cc_start: 0.9394 (mt0) cc_final: 0.9153 (mt0) REVERT: C 917 GLU cc_start: 0.9328 (mt-10) cc_final: 0.8984 (mt-10) REVERT: C 959 LEU cc_start: 0.9323 (tp) cc_final: 0.8851 (tp) REVERT: C 1062 ASN cc_start: 0.7832 (t0) cc_final: 0.6973 (t0) REVERT: C 1064 PHE cc_start: 0.8221 (m-80) cc_final: 0.7417 (m-80) REVERT: C 1078 LEU cc_start: 0.8180 (mt) cc_final: 0.7737 (tp) REVERT: C 1082 GLU cc_start: 0.9549 (mp0) cc_final: 0.9309 (mp0) REVERT: C 1104 GLN cc_start: 0.9145 (mt0) cc_final: 0.8455 (tm-30) REVERT: C 1108 ASP cc_start: 0.9025 (m-30) cc_final: 0.8391 (m-30) REVERT: C 1122 LYS cc_start: 0.8791 (mmtp) cc_final: 0.8441 (tppt) REVERT: C 1149 ASN cc_start: 0.9341 (t0) cc_final: 0.9037 (t0) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0647 time to fit residues: 13.2237 Evaluate side-chains 111 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [117, 64, 32, 135, 103, 202, 7, 28, 156, 2, 199] chunk 117 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 135 optimal weight: 0.0870 chunk 103 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 199 optimal weight: 0.6980 overall best weight: 2.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 868 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.053788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.040976 restraints weight = 48495.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.042612 restraints weight = 27651.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.043817 restraints weight = 18519.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.044597 restraints weight = 13639.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.045291 restraints weight = 10938.629| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28140 Z= 0.127 Angle : 0.511 6.942 38358 Z= 0.269 Chirality : 0.042 0.185 4320 Planarity : 0.004 0.073 4938 Dihedral : 3.984 18.618 3819 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: -0.04 (0.14), residues: 3489 helix: 1.46 (0.19), residues: 789 sheet: 0.29 (0.20), residues: 705 loop : -0.75 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 687 TYR 0.013 0.001 TYR A 684 PHE 0.009 0.001 PHE A 779 TRP 0.011 0.001 TRP A 460 HIS 0.003 0.001 HIS C 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (28077) covalent geometry : angle 0.50666 / 0.27 (38232) SS BOND : bond 0.00286 / 0.19 ( 63) SS BOND : angle 1.22772 / 0.80 ( 126) hydrogen bonds : bond 0.03521 / 2.33 ( 980) hydrogen bonds : angle 4.81221 / 3.27 ( 2976) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 LEU cc_start: 0.9599 (mt) cc_final: 0.9200 (mp) REVERT: C 78 MET cc_start: 0.9137 (mmm) cc_final: 0.8725 (mmm) REVERT: C 103 ILE cc_start: 0.9517 (pt) cc_final: 0.9286 (pt) REVERT: C 118 MET cc_start: 0.7919 (tpp) cc_final: 0.7432 (tpp) REVERT: C 379 ILE cc_start: 0.9357 (mm) cc_final: 0.9088 (mm) REVERT: C 387 ASN cc_start: 0.8971 (t0) cc_final: 0.8753 (t0) REVERT: C 397 MET cc_start: 0.8461 (mtm) cc_final: 0.8243 (mtm) REVERT: C 416 ASP cc_start: 0.9139 (m-30) cc_final: 0.8830 (m-30) REVERT: C 426 GLN cc_start: 0.9098 (mt0) cc_final: 0.8636 (mm-40) REVERT: C 469 ASP cc_start: 0.9521 (m-30) cc_final: 0.9122 (t0) REVERT: C 659 LEU cc_start: 0.8469 (tp) cc_final: 0.8240 (tp) REVERT: C 717 LEU cc_start: 0.9656 (mt) cc_final: 0.9393 (mp) REVERT: C 849 ASP cc_start: 0.9264 (m-30) cc_final: 0.8945 (p0) REVERT: C 852 ASN cc_start: 0.9551 (m-40) cc_final: 0.9197 (m-40) REVERT: C 859 ASN cc_start: 0.9541 (m-40) cc_final: 0.9293 (m-40) REVERT: C 889 PHE cc_start: 0.8202 (p90) cc_final: 0.7746 (p90) REVERT: C 917 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8961 (mt-10) REVERT: C 959 LEU cc_start: 0.9323 (tp) cc_final: 0.8868 (tp) REVERT: C 1021 PHE cc_start: 0.9541 (m-80) cc_final: 0.8936 (m-80) REVERT: C 1062 ASN cc_start: 0.7910 (t0) cc_final: 0.7062 (t0) REVERT: C 1064 PHE cc_start: 0.8427 (m-80) cc_final: 0.7564 (m-80) REVERT: C 1078 LEU cc_start: 0.8086 (mt) cc_final: 0.7649 (tp) REVERT: C 1082 GLU cc_start: 0.9572 (mp0) cc_final: 0.9351 (mp0) REVERT: C 1104 GLN cc_start: 0.9148 (mt0) cc_final: 0.8452 (tm-30) REVERT: C 1108 ASP cc_start: 0.9007 (m-30) cc_final: 0.8313 (m-30) REVERT: C 1122 LYS cc_start: 0.8802 (mmtp) cc_final: 0.8482 (tppt) REVERT: C 1149 ASN cc_start: 0.9339 (t0) cc_final: 0.9065 (t0) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0692 time to fit residues: 13.0033 Evaluate side-chains 104 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [1, 213, 125, 99, 318, 292, 192, 170, 236, 61, 66] chunk 1 optimal weight: 8.9990 chunk 213 optimal weight: 0.8980 chunk 125 optimal weight: 0.0870 chunk 99 optimal weight: 0.8980 chunk 318 optimal weight: 4.9990 chunk 292 optimal weight: 0.0770 chunk 192 optimal weight: 8.9990 chunk 170 optimal weight: 0.9980 chunk 236 optimal weight: 0.0040 chunk 61 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 overall best weight: 0.3528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.054860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.041820 restraints weight = 46564.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.043488 restraints weight = 26798.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.044721 restraints weight = 18042.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.045637 restraints weight = 13281.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.046297 restraints weight = 10447.951| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28140 Z= 0.092 Angle : 0.512 13.279 38358 Z= 0.260 Chirality : 0.042 0.155 4320 Planarity : 0.004 0.066 4938 Dihedral : 3.817 19.008 3819 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 0.10 (0.14), residues: 3489 helix: 1.57 (0.19), residues: 771 sheet: 0.42 (0.20), residues: 702 loop : -0.66 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 945 TYR 0.014 0.001 TYR A 424 PHE 0.014 0.001 PHE B1156 TRP 0.010 0.001 TRP B 460 HIS 0.002 0.001 HIS C 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (28077) covalent geometry : angle 0.50911 / 0.26 (38232) SS BOND : bond 0.00243 / 0.16 ( 63) SS BOND : angle 1.03861 / 0.66 ( 126) hydrogen bonds : bond 0.03315 / 2.19 ( 980) hydrogen bonds : angle 4.62205 / 3.14 ( 2976) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 LEU cc_start: 0.9570 (mt) cc_final: 0.9179 (mp) REVERT: C 78 MET cc_start: 0.9120 (mmm) cc_final: 0.8690 (mmm) REVERT: C 118 MET cc_start: 0.7876 (tpp) cc_final: 0.7367 (tpp) REVERT: C 168 MET cc_start: 0.8621 (ptp) cc_final: 0.7960 (pmm) REVERT: C 250 TYR cc_start: 0.8075 (t80) cc_final: 0.7070 (t80) REVERT: C 372 MET cc_start: 0.9239 (mmm) cc_final: 0.8829 (tpp) REVERT: C 376 MET cc_start: 0.9184 (ppp) cc_final: 0.8975 (ppp) REVERT: C 379 ILE cc_start: 0.9251 (mm) cc_final: 0.8895 (pt) REVERT: C 397 MET cc_start: 0.8362 (mtm) cc_final: 0.8130 (mtm) REVERT: C 416 ASP cc_start: 0.9039 (m-30) cc_final: 0.8758 (m-30) REVERT: C 426 GLN cc_start: 0.9124 (mt0) cc_final: 0.8579 (mm-40) REVERT: C 469 ASP cc_start: 0.9531 (m-30) cc_final: 0.9139 (t0) REVERT: C 659 LEU cc_start: 0.8136 (tp) cc_final: 0.7902 (tp) REVERT: C 717 LEU cc_start: 0.9655 (mt) cc_final: 0.9399 (mp) REVERT: C 852 ASN cc_start: 0.9548 (m-40) cc_final: 0.9191 (m110) REVERT: C 859 ASN cc_start: 0.9513 (m-40) cc_final: 0.9265 (m-40) REVERT: C 889 PHE cc_start: 0.8174 (p90) cc_final: 0.7710 (p90) REVERT: C 917 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8904 (mt-10) REVERT: C 959 LEU cc_start: 0.9321 (tp) cc_final: 0.8862 (tp) REVERT: C 1021 PHE cc_start: 0.9518 (m-80) cc_final: 0.8971 (m-80) REVERT: C 1062 ASN cc_start: 0.7823 (t0) cc_final: 0.7024 (t0) REVERT: C 1064 PHE cc_start: 0.8243 (m-80) cc_final: 0.7458 (m-80) REVERT: C 1078 LEU cc_start: 0.8114 (mt) cc_final: 0.7672 (tp) REVERT: C 1082 GLU cc_start: 0.9525 (mp0) cc_final: 0.9104 (mp0) REVERT: C 1104 GLN cc_start: 0.9158 (mt0) cc_final: 0.8435 (tm-30) REVERT: C 1108 ASP cc_start: 0.9003 (m-30) cc_final: 0.8351 (m-30) REVERT: C 1122 LYS cc_start: 0.8749 (mmtp) cc_final: 0.8396 (tppt) REVERT: C 1149 ASN cc_start: 0.9364 (t0) cc_final: 0.9047 (t0) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0698 time to fit residues: 14.4727 Evaluate side-chains 115 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [339, 269, 71, 294, 165, 89, 109, 176, 342, 63, 279] chunk 339 optimal weight: 0.9980 chunk 269 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 294 optimal weight: 0.7980 chunk 165 optimal weight: 0.0980 chunk 89 optimal weight: 0.7980 chunk 109 optimal weight: 0.0020 chunk 176 optimal weight: 1.9990 chunk 342 optimal weight: 0.0870 chunk 63 optimal weight: 8.9990 chunk 279 optimal weight: 3.9990 overall best weight: 0.3566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.054992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.041861 restraints weight = 46570.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.043541 restraints weight = 26961.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.044774 restraints weight = 18210.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.045674 restraints weight = 13461.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.046365 restraints weight = 10616.235| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 28140 Z= 0.090 Angle : 0.506 12.997 38358 Z= 0.260 Chirality : 0.042 0.155 4320 Planarity : 0.004 0.051 4938 Dihedral : 3.721 18.986 3819 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 0.11 (0.14), residues: 3489 helix: 1.33 (0.19), residues: 789 sheet: 0.43 (0.19), residues: 735 loop : -0.57 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 945 TYR 0.018 0.001 TYR A 424 PHE 0.009 0.001 PHE C 782 TRP 0.010 0.001 TRP B 460 HIS 0.002 0.000 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (28077) covalent geometry : angle 0.50389 / 0.26 (38232) SS BOND : bond 0.00274 / 0.16 ( 63) SS BOND : angle 1.00661 / 0.64 ( 126) hydrogen bonds : bond 0.03257 / 2.15 ( 980) hydrogen bonds : angle 4.57098 / 3.10 ( 2976) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 LEU cc_start: 0.9338 (tp) cc_final: 0.9012 (tp) REVERT: C 64 LEU cc_start: 0.9580 (mt) cc_final: 0.9166 (mp) REVERT: C 78 MET cc_start: 0.9104 (mmm) cc_final: 0.8685 (mmm) REVERT: C 118 MET cc_start: 0.7927 (tpp) cc_final: 0.7417 (tpp) REVERT: C 250 TYR cc_start: 0.8100 (t80) cc_final: 0.7082 (t80) REVERT: C 372 MET cc_start: 0.9287 (mmm) cc_final: 0.8821 (tpp) REVERT: C 376 MET cc_start: 0.9327 (ppp) cc_final: 0.9023 (ppp) REVERT: C 379 ILE cc_start: 0.9169 (mm) cc_final: 0.8904 (pt) REVERT: C 397 MET cc_start: 0.8395 (mtm) cc_final: 0.8142 (mtm) REVERT: C 416 ASP cc_start: 0.9007 (m-30) cc_final: 0.8760 (m-30) REVERT: C 426 GLN cc_start: 0.9157 (mt0) cc_final: 0.8641 (mm-40) REVERT: C 452 VAL cc_start: 0.9272 (t) cc_final: 0.9056 (p) REVERT: C 469 ASP cc_start: 0.9537 (m-30) cc_final: 0.9146 (t0) REVERT: C 559 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7353 (mp0) REVERT: C 659 LEU cc_start: 0.8197 (tp) cc_final: 0.7969 (tp) REVERT: C 717 LEU cc_start: 0.9658 (mt) cc_final: 0.9403 (mp) REVERT: C 852 ASN cc_start: 0.9523 (m-40) cc_final: 0.9156 (m110) REVERT: C 859 ASN cc_start: 0.9485 (m-40) cc_final: 0.9246 (m-40) REVERT: C 889 PHE cc_start: 0.8161 (p90) cc_final: 0.7686 (p90) REVERT: C 917 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8891 (mt-10) REVERT: C 959 LEU cc_start: 0.9309 (tp) cc_final: 0.8857 (tp) REVERT: C 1062 ASN cc_start: 0.7795 (t0) cc_final: 0.6955 (t0) REVERT: C 1078 LEU cc_start: 0.8071 (mt) cc_final: 0.7629 (tp) REVERT: C 1082 GLU cc_start: 0.9530 (mp0) cc_final: 0.9090 (mp0) REVERT: C 1104 GLN cc_start: 0.9167 (mt0) cc_final: 0.8481 (tm-30) REVERT: C 1108 ASP cc_start: 0.9010 (m-30) cc_final: 0.8376 (m-30) REVERT: C 1122 LYS cc_start: 0.8743 (mmtp) cc_final: 0.8368 (tppt) REVERT: C 1149 ASN cc_start: 0.9403 (t0) cc_final: 0.9085 (t0) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0661 time to fit residues: 13.3042 Evaluate side-chains 112 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [163, 340, 16, 276, 221, 118, 60, 200, 175, 29, 122] chunk 163 optimal weight: 9.9990 chunk 340 optimal weight: 0.5980 chunk 16 optimal weight: 0.0870 chunk 276 optimal weight: 0.0670 chunk 221 optimal weight: 0.7980 chunk 118 optimal weight: 0.4980 chunk 60 optimal weight: 0.0170 chunk 200 optimal weight: 0.1980 chunk 175 optimal weight: 0.0050 chunk 29 optimal weight: 5.9990 chunk 122 optimal weight: 0.0870 overall best weight: 0.0526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.055734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.042579 restraints weight = 45997.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.044249 restraints weight = 26741.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.045477 restraints weight = 18151.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.046404 restraints weight = 13419.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.047095 restraints weight = 10563.728| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 28140 Z= 0.090 Angle : 0.515 13.057 38358 Z= 0.262 Chirality : 0.042 0.158 4320 Planarity : 0.004 0.054 4938 Dihedral : 3.633 18.858 3819 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: 0.11 (0.14), residues: 3489 helix: 1.23 (0.19), residues: 789 sheet: 0.48 (0.19), residues: 735 loop : -0.54 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 670 TYR 0.019 0.001 TYR C 424 PHE 0.009 0.001 PHE C 782 TRP 0.011 0.001 TRP B 460 HIS 0.002 0.000 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (28077) covalent geometry : angle 0.51239 / 0.26 (38232) SS BOND : bond 0.00202 / 0.13 ( 63) SS BOND : angle 1.05526 / 0.66 ( 126) hydrogen bonds : bond 0.03195 / 2.11 ( 980) hydrogen bonds : angle 4.48872 / 3.05 ( 2976) *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 LEU cc_start: 0.9340 (tp) cc_final: 0.9117 (tp) REVERT: C 78 MET cc_start: 0.9069 (mmm) cc_final: 0.8670 (mmm) REVERT: C 103 ILE cc_start: 0.9676 (pt) cc_final: 0.9430 (pt) REVERT: C 118 MET cc_start: 0.7878 (tpp) cc_final: 0.7357 (mmp) REVERT: C 250 TYR cc_start: 0.8046 (t80) cc_final: 0.7030 (t80) REVERT: C 372 MET cc_start: 0.9259 (mmm) cc_final: 0.8849 (tpp) REVERT: C 376 MET cc_start: 0.9272 (ppp) cc_final: 0.9019 (ppp) REVERT: C 379 ILE cc_start: 0.9147 (mm) cc_final: 0.8910 (pt) REVERT: C 416 ASP cc_start: 0.8989 (m-30) cc_final: 0.8756 (m-30) REVERT: C 426 GLN cc_start: 0.9131 (mt0) cc_final: 0.8606 (mm-40) REVERT: C 452 VAL cc_start: 0.9226 (t) cc_final: 0.9001 (p) REVERT: C 469 ASP cc_start: 0.9524 (m-30) cc_final: 0.9145 (t0) REVERT: C 659 LEU cc_start: 0.8172 (tp) cc_final: 0.7951 (tp) REVERT: C 852 ASN cc_start: 0.9505 (m-40) cc_final: 0.9143 (m110) REVERT: C 859 ASN cc_start: 0.9451 (m-40) cc_final: 0.9213 (m-40) REVERT: C 889 PHE cc_start: 0.8175 (p90) cc_final: 0.7684 (p90) REVERT: C 959 LEU cc_start: 0.9337 (tp) cc_final: 0.8891 (tp) REVERT: C 1062 ASN cc_start: 0.7679 (t0) cc_final: 0.6768 (t0) REVERT: C 1078 LEU cc_start: 0.8157 (mt) cc_final: 0.7711 (tp) REVERT: C 1082 GLU cc_start: 0.9522 (mp0) cc_final: 0.9046 (mp0) REVERT: C 1104 GLN cc_start: 0.9162 (mt0) cc_final: 0.8426 (tm-30) REVERT: C 1108 ASP cc_start: 0.8971 (m-30) cc_final: 0.8332 (m-30) REVERT: C 1121 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8250 (pt0) REVERT: C 1122 LYS cc_start: 0.8744 (mmtp) cc_final: 0.8336 (tppt) REVERT: C 1149 ASN cc_start: 0.9417 (t0) cc_final: 0.9028 (t0) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.0674 time to fit residues: 14.1356 Evaluate side-chains 115 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [179, 349, 225, 97, 321, 220, 189, 132, 129, 38, 205] chunk 179 optimal weight: 6.9990 chunk 349 optimal weight: 8.9990 chunk 225 optimal weight: 0.9980 chunk 97 optimal weight: 0.0070 chunk 321 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 189 optimal weight: 0.4980 chunk 132 optimal weight: 0.8980 chunk 129 optimal weight: 0.0030 chunk 38 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 overall best weight: 0.4808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.055818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.043015 restraints weight = 46529.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.044629 restraints weight = 27507.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.045796 restraints weight = 18743.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.046686 restraints weight = 13947.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.047294 restraints weight = 11044.382| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28140 Z= 0.090 Angle : 0.522 12.904 38358 Z= 0.266 Chirality : 0.042 0.219 4320 Planarity : 0.004 0.050 4938 Dihedral : 3.630 18.459 3819 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 0.16 (0.14), residues: 3489 helix: 1.28 (0.19), residues: 789 sheet: 0.62 (0.19), residues: 750 loop : -0.57 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 945 TYR 0.014 0.001 TYR C 424 PHE 0.017 0.001 PHE B1021 TRP 0.033 0.001 TRP A 460 HIS 0.002 0.000 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (28077) covalent geometry : angle 0.51937 / 0.26 (38232) SS BOND : bond 0.00199 / 0.12 ( 63) SS BOND : angle 1.05047 / 0.66 ( 126) hydrogen bonds : bond 0.03254 / 2.15 ( 980) hydrogen bonds : angle 4.46395 / 3.03 ( 2976) ********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.259 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: C 64 LEU cc_start: 0.9658 (mt) cc_final: 0.9332 (mp) REVERT: C 78 MET cc_start: 0.9057 (mmm) cc_final: 0.8645 (mmm) REVERT: C 118 MET cc_start: 0.7913 (tpp) cc_final: 0.7492 (mmp) REVERT: C 250 TYR cc_start: 0.8014 (t80) cc_final: 0.6996 (t80) REVERT: C 284 ILE cc_start: 0.9694 (mt) cc_final: 0.9223 (tp) REVERT: C 372 MET cc_start: 0.9263 (mmm) cc_final: 0.8815 (tpp) REVERT: C 376 MET cc_start: 0.9278 (ppp) cc_final: 0.9018 (ppp) REVERT: C 379 ILE cc_start: 0.9132 (mm) cc_final: 0.8910 (pt) REVERT: C 416 ASP cc_start: 0.8989 (m-30) cc_final: 0.8756 (m-30) REVERT: C 426 GLN cc_start: 0.9085 (mt0) cc_final: 0.8594 (mm-40) REVERT: C 452 VAL cc_start: 0.9250 (t) cc_final: 0.9029 (p) REVERT: C 469 ASP cc_start: 0.9509 (m-30) cc_final: 0.9136 (t0) REVERT: C 659 LEU cc_start: 0.8166 (tp) cc_final: 0.7928 (tp) REVERT: C 852 ASN cc_start: 0.9507 (m-40) cc_final: 0.9142 (m110) REVERT: C 859 ASN cc_start: 0.9397 (m-40) cc_final: 0.9144 (m-40) REVERT: C 889 PHE cc_start: 0.8204 (p90) cc_final: 0.7716 (p90) REVERT: C 913 ARG cc_start: 0.9128 (mtt90) cc_final: 0.8654 (mtm-85) REVERT: C 959 LEU cc_start: 0.9330 (tp) cc_final: 0.8881 (tp) REVERT: C 1021 PHE cc_start: 0.9516 (m-80) cc_final: 0.8956 (m-80) REVERT: C 1062 ASN cc_start: 0.7722 (t0) cc_final: 0.6799 (t0) REVERT: C 1078 LEU cc_start: 0.8229 (mt) cc_final: 0.7803 (tp) REVERT: C 1082 GLU cc_start: 0.9508 (mp0) cc_final: 0.9034 (mp0) REVERT: C 1104 GLN cc_start: 0.9155 (mt0) cc_final: 0.8416 (tm-30) REVERT: C 1108 ASP cc_start: 0.8940 (m-30) cc_final: 0.8290 (m-30) REVERT: C 1121 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8295 (pt0) REVERT: C 1122 LYS cc_start: 0.8724 (mmtp) cc_final: 0.8479 (mttp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.0626 time to fit residues: 13.5938 Evaluate side-chains 112 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: [123, 40, 23, 204, 189, 3, 196, 150, 68, 184, 249] chunk 123 optimal weight: 0.2980 chunk 40 optimal weight: 0.0170 chunk 23 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 184 optimal weight: 8.9990 chunk 249 optimal weight: 5.9990 overall best weight: 1.8624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.054825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.042107 restraints weight = 47634.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.043670 restraints weight = 28186.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.044828 restraints weight = 19326.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.045674 restraints weight = 14374.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.046312 restraints weight = 11412.288| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28140 Z= 0.114 Angle : 0.529 8.552 38358 Z= 0.276 Chirality : 0.043 0.235 4320 Planarity : 0.004 0.048 4938 Dihedral : 3.717 16.818 3819 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 0.19 (0.14), residues: 3489 helix: 1.45 (0.19), residues: 783 sheet: 0.52 (0.19), residues: 765 loop : -0.58 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 945 TYR 0.014 0.001 TYR C 424 PHE 0.025 0.001 PHE A 782 TRP 0.032 0.001 TRP A 460 HIS 0.002 0.001 HIS C 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (28077) covalent geometry : angle 0.52362 / 0.27 (38232) SS BOND : bond 0.00239 / 0.15 ( 63) SS BOND : angle 1.41879 / 0.90 ( 126) hydrogen bonds : bond 0.03304 / 2.19 ( 980) hydrogen bonds : angle 4.54148 / 3.09 ( 2976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2322.95 seconds wall clock time: 41 minutes 49.65 seconds (2509.65 seconds total)