Starting phenix.real_space_refine on Wed Nov 19 14:41:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6acc_9588/11_2025/6acc_9588.cif Found real_map, /net/cci-nas-00/data/ceres_data/6acc_9588/11_2025/6acc_9588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6acc_9588/11_2025/6acc_9588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6acc_9588/11_2025/6acc_9588.map" model { file = "/net/cci-nas-00/data/ceres_data/6acc_9588/11_2025/6acc_9588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6acc_9588/11_2025/6acc_9588.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 135 5.16 5 C 15912 2.51 5 N 4122 2.21 5 O 4737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24906 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Chain: "B" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Chain: "C" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Time building chain proxies: 5.70, per 1000 atoms: 0.23 Number of scatterers: 24906 At special positions: 0 Unit cell: (149.16, 147.84, 161.04, 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 135 16.00 O 4737 8.00 N 4122 7.00 C 15912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.04 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.02 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.04 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.02 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.04 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.02 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.04 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.02 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.04 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.02 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.04 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.04 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.04 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.02 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.04 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.04 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: 2.02 Conformation dependent library (CDL) restraints added in 1.2 seconds 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5988 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 42 sheets defined 20.7% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.913A pdb=" N ASP A 376 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 377 " --> pdb=" O LEU A 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 373 through 377' Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 740 through 764 Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.835A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 865 Processing helix chain 'A' and resid 880 through 887 removed outlier: 3.626A pdb=" N MET A 884 " --> pdb=" O PHE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 890 No H-bonds generated for 'chain 'A' and resid 888 through 890' Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.049A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 900 " --> pdb=" O ASN A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 removed outlier: 3.903A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 950 removed outlier: 3.734A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 949 " --> pdb=" O VAL A 945 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 950 " --> pdb=" O LYS A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 removed outlier: 4.294A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1014 removed outlier: 3.723A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 373 through 377 removed outlier: 3.913A pdb=" N ASP B 376 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 373 through 377' Processing helix chain 'B' and resid 392 through 397 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 604 through 612 Processing helix chain 'B' and resid 730 through 737 Processing helix chain 'B' and resid 740 through 764 Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.836A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 865 Processing helix chain 'B' and resid 880 through 887 removed outlier: 3.626A pdb=" N MET B 884 " --> pdb=" O PHE B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 890 No H-bonds generated for 'chain 'B' and resid 888 through 890' Processing helix chain 'B' and resid 895 through 901 removed outlier: 4.049A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 900 " --> pdb=" O ASN B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 removed outlier: 3.904A pdb=" N THR B 921 " --> pdb=" O GLN B 917 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 950 removed outlier: 3.735A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 949 " --> pdb=" O VAL B 945 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 950 " --> pdb=" O LYS B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 966 removed outlier: 4.294A pdb=" N ARG B 965 " --> pdb=" O ASP B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 1014 removed outlier: 3.722A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 373 through 377 removed outlier: 3.913A pdb=" N ASP C 376 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU C 377 " --> pdb=" O LEU C 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 373 through 377' Processing helix chain 'C' and resid 392 through 397 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 604 through 612 Processing helix chain 'C' and resid 730 through 737 Processing helix chain 'C' and resid 740 through 764 Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.796A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 865 Processing helix chain 'C' and resid 880 through 887 removed outlier: 3.625A pdb=" N MET C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 890 No H-bonds generated for 'chain 'C' and resid 888 through 890' Processing helix chain 'C' and resid 895 through 901 removed outlier: 4.050A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 900 " --> pdb=" O ASN C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 removed outlier: 3.903A pdb=" N THR C 921 " --> pdb=" O GLN C 917 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 950 removed outlier: 3.735A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 950 " --> pdb=" O LYS C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 966 removed outlier: 4.294A pdb=" N ARG C 965 " --> pdb=" O ASP C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 1014 removed outlier: 3.722A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 34 removed outlier: 3.824A pdb=" N THR A 31 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 66 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 254 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 71 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA A 250 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 90 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 255 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 190 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.698A pdb=" N LEU A 264 " --> pdb=" O TYR A 53 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP A 57 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR A 260 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 59 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.518A pdb=" N SER A 113 " --> pdb=" O CYS A 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 141 removed outlier: 5.759A pdb=" N PHE A 138 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER A 239 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 298 through 301 removed outlier: 3.738A pdb=" N GLY A 298 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR A 585 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 300 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314 removed outlier: 3.548A pdb=" N PHE A 527 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR A 539 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.552A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A 419 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 441 removed outlier: 3.589A pdb=" N ASN A 479 " --> pdb=" O TYR A 440 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 650 through 651 Processing sheet with id=AB1, first strand: chain 'A' and resid 683 through 684 removed outlier: 6.121A pdb=" N ALA A 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 709 removed outlier: 3.655A pdb=" N SER A 703 " --> pdb=" O THR A1048 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A1048 " --> pdb=" O SER A 703 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 707 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A1041 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A1038 " --> pdb=" O GLY A1041 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB4, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AB5, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 4.064A pdb=" N PHE A1071 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A1103 " --> pdb=" O PHE A1071 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1078 through 1079 Processing sheet with id=AB7, first strand: chain 'B' and resid 31 through 34 removed outlier: 3.825A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 66 " --> pdb=" O HIS B 33 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 254 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 71 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA B 250 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 90 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 255 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL B 186 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B 190 " --> pdb=" O PHE B 193 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.698A pdb=" N LEU B 264 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP B 57 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR B 260 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B 59 " --> pdb=" O LYS B 258 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.519A pdb=" N SER B 113 " --> pdb=" O CYS B 128 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 138 through 141 removed outlier: 5.759A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 298 through 301 removed outlier: 3.737A pdb=" N GLY B 298 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR B 585 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 300 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 313 through 314 removed outlier: 3.548A pdb=" N PHE B 527 " --> pdb=" O GLY B 534 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY B 534 " --> pdb=" O PHE B 527 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 539 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.552A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS B 419 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 439 through 441 removed outlier: 3.589A pdb=" N ASN B 479 " --> pdb=" O TYR B 440 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 709 removed outlier: 3.654A pdb=" N SER B 703 " --> pdb=" O THR B1048 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B1048 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 707 " --> pdb=" O PHE B1044 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B1041 " --> pdb=" O ALA B1038 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B1038 " --> pdb=" O GLY B1041 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AC9, first strand: chain 'B' and resid 769 through 770 Processing sheet with id=AD1, first strand: chain 'B' and resid 1063 through 1064 removed outlier: 4.064A pdb=" N PHE B1071 " --> pdb=" O PHE B1103 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE B1103 " --> pdb=" O PHE B1071 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1078 through 1079 Processing sheet with id=AD3, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.825A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 66 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 254 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR C 71 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA C 250 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 90 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 255 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL C 186 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 190 " --> pdb=" O PHE C 193 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.697A pdb=" N LEU C 264 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP C 57 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR C 260 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE C 59 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.518A pdb=" N SER C 113 " --> pdb=" O CYS C 128 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 138 through 141 removed outlier: 5.760A pdb=" N PHE C 138 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER C 239 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 298 through 301 removed outlier: 3.738A pdb=" N GLY C 298 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR C 585 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR C 300 " --> pdb=" O VAL C 583 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 313 through 314 removed outlier: 3.548A pdb=" N PHE C 527 " --> pdb=" O GLY C 534 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY C 534 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR C 539 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.552A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS C 419 " --> pdb=" O LEU C 499 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 439 through 441 removed outlier: 3.589A pdb=" N ASN C 479 " --> pdb=" O TYR C 440 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 650 through 651 Processing sheet with id=AE3, first strand: chain 'C' and resid 701 through 709 removed outlier: 3.656A pdb=" N SER C 703 " --> pdb=" O THR C1048 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C1048 " --> pdb=" O SER C 703 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU C 707 " --> pdb=" O PHE C1044 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY C1041 " --> pdb=" O ALA C1038 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA C1038 " --> pdb=" O GLY C1041 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AE5, first strand: chain 'C' and resid 1063 through 1064 removed outlier: 4.064A pdb=" N PHE C1071 " --> pdb=" O PHE C1103 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE C1103 " --> pdb=" O PHE C1071 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1078 through 1079 779 hydrogen bonds defined for protein. 2085 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: 5.92 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4085 1.28 - 1.42: 6849 1.42 - 1.56: 14377 1.56 - 1.70: 3 1.70 - 1.84: 183 Bond restraints: 25497 Sorted by residual: bond pdb=" C LEU C 804 " pdb=" O LEU C 804 " ideal model delta sigma weight residual 1.237 1.146 0.091 1.16e-02 7.43e+03 6.12e+01 bond pdb=" CA LEU C 804 " pdb=" C LEU C 804 " ideal model delta sigma weight residual 1.524 1.450 0.074 1.26e-02 6.30e+03 3.42e+01 bond pdb=" N PHE C 805 " pdb=" CA PHE C 805 " ideal model delta sigma weight residual 1.459 1.391 0.068 1.23e-02 6.61e+03 3.04e+01 bond pdb=" C LEU C 804 " pdb=" N PHE C 805 " ideal model delta sigma weight residual 1.335 1.277 0.058 1.30e-02 5.92e+03 2.01e+01 bond pdb=" CD ARG B 797 " pdb=" NE ARG B 797 " ideal model delta sigma weight residual 1.458 1.400 0.058 1.40e-02 5.10e+03 1.71e+01 ... (remaining 25492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 32856 1.89 - 3.79: 1508 3.79 - 5.68: 241 5.68 - 7.58: 63 7.58 - 9.47: 36 Bond angle restraints: 34704 Sorted by residual: angle pdb=" N LEU C 804 " pdb=" CA LEU C 804 " pdb=" C LEU C 804 " ideal model delta sigma weight residual 111.14 103.35 7.79 1.08e+00 8.57e-01 5.21e+01 angle pdb=" C LEU C 804 " pdb=" N PHE C 805 " pdb=" CA PHE C 805 " ideal model delta sigma weight residual 120.38 112.41 7.97 1.37e+00 5.33e-01 3.38e+01 angle pdb=" N ASP C 961 " pdb=" CA ASP C 961 " pdb=" C ASP C 961 " ideal model delta sigma weight residual 114.04 107.12 6.92 1.24e+00 6.50e-01 3.11e+01 angle pdb=" N ASP A 961 " pdb=" CA ASP A 961 " pdb=" C ASP A 961 " ideal model delta sigma weight residual 114.04 107.12 6.92 1.24e+00 6.50e-01 3.11e+01 angle pdb=" N ASP B 961 " pdb=" CA ASP B 961 " pdb=" C ASP B 961 " ideal model delta sigma weight residual 114.04 107.16 6.88 1.24e+00 6.50e-01 3.08e+01 ... (remaining 34699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 14566 17.68 - 35.36: 462 35.36 - 53.04: 100 53.04 - 70.72: 25 70.72 - 88.40: 9 Dihedral angle restraints: 15162 sinusoidal: 5850 harmonic: 9312 Sorted by residual: dihedral pdb=" CA GLU B1074 " pdb=" C GLU B1074 " pdb=" N GLY B1075 " pdb=" CA GLY B1075 " ideal model delta harmonic sigma weight residual -180.00 -121.08 -58.92 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA GLU C1074 " pdb=" C GLU C1074 " pdb=" N GLY C1075 " pdb=" CA GLY C1075 " ideal model delta harmonic sigma weight residual -180.00 -121.09 -58.91 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA GLU A1074 " pdb=" C GLU A1074 " pdb=" N GLY A1075 " pdb=" CA GLY A1075 " ideal model delta harmonic sigma weight residual -180.00 -121.12 -58.88 0 5.00e+00 4.00e-02 1.39e+02 ... (remaining 15159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2880 0.059 - 0.117: 840 0.117 - 0.176: 187 0.176 - 0.235: 21 0.235 - 0.294: 2 Chirality restraints: 3930 Sorted by residual: chirality pdb=" CA ARG A 797 " pdb=" N ARG A 797 " pdb=" C ARG A 797 " pdb=" CB ARG A 797 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA PHE C 805 " pdb=" N PHE C 805 " pdb=" C PHE C 805 " pdb=" CB PHE C 805 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASN A1117 " pdb=" N ASN A1117 " pdb=" C ASN A1117 " pdb=" CB ASN A1117 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 3927 not shown) Planarity restraints: 4497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 797 " -0.015 2.00e-02 2.50e+03 3.14e-02 9.88e+00 pdb=" C ARG B 797 " 0.054 2.00e-02 2.50e+03 pdb=" O ARG B 797 " -0.021 2.00e-02 2.50e+03 pdb=" N SER B 798 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 678 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.07e+00 pdb=" C THR C 678 " 0.052 2.00e-02 2.50e+03 pdb=" O THR C 678 " -0.019 2.00e-02 2.50e+03 pdb=" N MET C 679 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 678 " -0.015 2.00e-02 2.50e+03 3.00e-02 8.98e+00 pdb=" C THR A 678 " 0.052 2.00e-02 2.50e+03 pdb=" O THR A 678 " -0.019 2.00e-02 2.50e+03 pdb=" N MET A 679 " -0.018 2.00e-02 2.50e+03 ... (remaining 4494 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 754 2.69 - 3.24: 22914 3.24 - 3.80: 37195 3.80 - 4.35: 49007 4.35 - 4.90: 80924 Nonbonded interactions: 190794 Sorted by model distance: nonbonded pdb=" NH2 ARG A 797 " pdb=" CD2 PHE A 805 " model vdw 2.139 3.420 nonbonded pdb=" CB PRO A 789 " pdb=" O ARG A 797 " model vdw 2.172 3.440 nonbonded pdb=" NH2 ARG C 797 " pdb=" CD2 PHE C 805 " model vdw 2.237 3.420 nonbonded pdb=" OD1 ASN B 896 " pdb=" OG SER C1105 " model vdw 2.282 3.040 nonbonded pdb=" O GLN A 939 " pdb=" OG1 THR A 943 " model vdw 2.297 3.040 ... (remaining 190789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.750 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 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 : 0.005 0.097 25536 Z= 0.263 Angle : 0.957 9.470 34782 Z= 0.544 Chirality : 0.059 0.294 3930 Planarity : 0.008 0.066 4497 Dihedral : 9.618 78.319 9057 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.60 % Allowed : 11.95 % Favored : 87.45 % Rotamer: Outliers : 0.43 % Allowed : 1.55 % Favored : 98.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -4.74 (0.12), residues: 3171 helix: -1.84 (0.17), residues: 567 sheet: -2.99 (0.20), residues: 483 loop : -3.84 (0.10), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 797 TYR 0.015 0.002 TYR B 252 PHE 0.047 0.003 PHE C 837 TRP 0.018 0.002 TRP C 868 HIS 0.009 0.002 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00539 (25497) covalent geometry : angle 0.95465 (34704) SS BOND : bond 0.00767 ( 39) SS BOND : angle 1.75582 ( 78) hydrogen bonds : bond 0.23320 ( 779) hydrogen bonds : angle 9.05659 ( 2085) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 701 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 SER cc_start: 0.7922 (t) cc_final: 0.7266 (p) REVERT: A 214 ASN cc_start: 0.8014 (t0) cc_final: 0.7697 (t0) REVERT: A 226 ILE cc_start: 0.7312 (pt) cc_final: 0.7093 (pt) REVERT: A 229 THR cc_start: 0.7165 (p) cc_final: 0.6963 (p) REVERT: A 230 ASN cc_start: 0.7092 (m-40) cc_final: 0.6854 (m-40) REVERT: A 261 THR cc_start: 0.8561 (m) cc_final: 0.8300 (p) REVERT: A 361 PHE cc_start: 0.7506 (m-10) cc_final: 0.7134 (m-80) REVERT: A 365 LYS cc_start: 0.7608 (tttt) cc_final: 0.7326 (mmtt) REVERT: A 372 THR cc_start: 0.8462 (p) cc_final: 0.8179 (p) REVERT: A 387 PHE cc_start: 0.8043 (p90) cc_final: 0.7782 (p90) REVERT: A 454 ASP cc_start: 0.7140 (m-30) cc_final: 0.6443 (p0) REVERT: A 797 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6624 (mtm-85) REVERT: A 1116 ASN cc_start: 0.7771 (m-40) cc_final: 0.7461 (p0) REVERT: B 49 SER cc_start: 0.7961 (t) cc_final: 0.7531 (p) REVERT: B 131 GLU cc_start: 0.6858 (tt0) cc_final: 0.6655 (tp30) REVERT: B 184 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7284 (tt0) REVERT: B 214 ASN cc_start: 0.7669 (t0) cc_final: 0.7347 (t0) REVERT: B 230 ASN cc_start: 0.7016 (m-40) cc_final: 0.6791 (m-40) REVERT: B 258 LYS cc_start: 0.8051 (tttt) cc_final: 0.7622 (ttmm) REVERT: B 361 PHE cc_start: 0.7513 (m-10) cc_final: 0.7258 (m-10) REVERT: B 365 LYS cc_start: 0.7575 (tttt) cc_final: 0.7196 (mmtm) REVERT: B 367 TYR cc_start: 0.7626 (m-10) cc_final: 0.7366 (m-10) REVERT: B 372 THR cc_start: 0.8262 (p) cc_final: 0.7970 (p) REVERT: B 387 PHE cc_start: 0.8105 (p90) cc_final: 0.7789 (p90) REVERT: B 454 ASP cc_start: 0.7275 (m-30) cc_final: 0.6464 (p0) REVERT: B 500 SER cc_start: 0.9030 (t) cc_final: 0.8586 (p) REVERT: B 573 ILE cc_start: 0.7385 (mt) cc_final: 0.7101 (mt) REVERT: B 837 PHE cc_start: 0.7037 (p90) cc_final: 0.6808 (p90) REVERT: B 841 THR cc_start: 0.8821 (t) cc_final: 0.8523 (m) REVERT: B 1019 SER cc_start: 0.8503 (t) cc_final: 0.8279 (m) REVERT: C 49 SER cc_start: 0.8031 (t) cc_final: 0.7190 (p) REVERT: C 361 PHE cc_start: 0.7421 (m-10) cc_final: 0.7208 (m-10) REVERT: C 372 THR cc_start: 0.8290 (p) cc_final: 0.8027 (p) REVERT: C 387 PHE cc_start: 0.8043 (p90) cc_final: 0.7736 (p90) REVERT: C 454 ASP cc_start: 0.7287 (m-30) cc_final: 0.6141 (p0) REVERT: C 497 VAL cc_start: 0.8913 (t) cc_final: 0.8687 (p) REVERT: C 500 SER cc_start: 0.8999 (t) cc_final: 0.8531 (p) REVERT: C 527 PHE cc_start: 0.7003 (m-10) cc_final: 0.6718 (m-80) REVERT: C 562 VAL cc_start: 0.8118 (m) cc_final: 0.7909 (p) REVERT: C 837 PHE cc_start: 0.7151 (p90) cc_final: 0.6407 (p90) REVERT: C 1013 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6760 (mm-30) REVERT: C 1116 ASN cc_start: 0.8108 (m-40) cc_final: 0.7882 (p0) outliers start: 12 outliers final: 1 residues processed: 708 average time/residue: 0.1835 time to fit residues: 200.0754 Evaluate side-chains 381 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 379 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain C residue 797 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 181 HIS A 321 ASN A 721 ASN A 766 GLN A 987 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 149 HIS B 181 HIS B 321 ASN B 721 ASN B 766 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 HIS C 181 HIS C 214 ASN C 321 ASN C 737 GLN C 744 GLN C 766 GLN C 939 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.173375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132457 restraints weight = 41220.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133904 restraints weight = 22224.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.135494 restraints weight = 17049.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.136242 restraints weight = 13378.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.136796 restraints weight = 11798.652| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 25536 Z= 0.262 Angle : 0.836 14.355 34782 Z= 0.445 Chirality : 0.051 0.257 3930 Planarity : 0.006 0.059 4497 Dihedral : 7.345 54.328 3440 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.54 % Allowed : 13.40 % Favored : 86.06 % Rotamer: Outliers : 3.47 % Allowed : 9.07 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -3.93 (0.13), residues: 3171 helix: -0.03 (0.20), residues: 555 sheet: -2.46 (0.20), residues: 570 loop : -3.66 (0.11), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 758 TYR 0.023 0.002 TYR A 689 PHE 0.027 0.002 PHE A 364 TRP 0.015 0.002 TRP A 423 HIS 0.011 0.002 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00617 (25497) covalent geometry : angle 0.82086 (34704) SS BOND : bond 0.01042 ( 39) SS BOND : angle 3.44924 ( 78) hydrogen bonds : bond 0.05134 ( 779) hydrogen bonds : angle 6.78999 ( 2085) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 396 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 214 ASN cc_start: 0.8075 (t0) cc_final: 0.7625 (t0) REVERT: A 454 ASP cc_start: 0.7215 (m-30) cc_final: 0.6626 (p0) REVERT: A 483 PHE cc_start: 0.7476 (m-10) cc_final: 0.7064 (m-80) REVERT: A 641 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7927 (t-90) REVERT: A 687 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8252 (pp) REVERT: A 882 MET cc_start: 0.7958 (mtp) cc_final: 0.7563 (mtp) REVERT: A 996 ARG cc_start: 0.7828 (ttm110) cc_final: 0.7560 (ttm-80) REVERT: A 1011 MET cc_start: 0.9212 (tpp) cc_final: 0.8992 (tpp) REVERT: B 131 GLU cc_start: 0.6864 (tt0) cc_final: 0.6615 (tp30) REVERT: B 184 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7172 (tt0) REVERT: B 214 ASN cc_start: 0.7768 (t0) cc_final: 0.7292 (t0) REVERT: B 258 LYS cc_start: 0.8159 (tttt) cc_final: 0.7622 (ttmm) REVERT: B 387 PHE cc_start: 0.8095 (p90) cc_final: 0.7785 (p90) REVERT: B 454 ASP cc_start: 0.7118 (m-30) cc_final: 0.6520 (p0) REVERT: B 523 GLN cc_start: 0.8343 (tt0) cc_final: 0.7827 (tt0) REVERT: B 841 THR cc_start: 0.8656 (t) cc_final: 0.8439 (m) REVERT: B 1077 PHE cc_start: 0.5315 (t80) cc_final: 0.4846 (t80) REVERT: C 184 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7367 (mt-10) REVERT: C 214 ASN cc_start: 0.7675 (t0) cc_final: 0.7361 (t0) REVERT: C 387 PHE cc_start: 0.8145 (p90) cc_final: 0.7724 (p90) REVERT: C 454 ASP cc_start: 0.7163 (m-30) cc_final: 0.6496 (p0) REVERT: C 523 GLN cc_start: 0.8408 (tt0) cc_final: 0.7886 (tt0) REVERT: C 687 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7982 (pp) REVERT: C 766 GLN cc_start: 0.8147 (mt0) cc_final: 0.7896 (mt0) REVERT: C 837 PHE cc_start: 0.7014 (p90) cc_final: 0.5675 (p90) REVERT: C 882 MET cc_start: 0.7652 (mtp) cc_final: 0.7331 (mtp) outliers start: 96 outliers final: 62 residues processed: 463 average time/residue: 0.1609 time to fit residues: 120.8622 Evaluate side-chains 369 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 304 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 779 PHE Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 58 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 301 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 45 optimal weight: 0.0060 chunk 128 optimal weight: 20.0000 chunk 267 optimal weight: 2.9990 chunk 237 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 744 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 230 ASN ** B1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN C 321 ASN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.174725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.134042 restraints weight = 41162.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.135770 restraints weight = 22240.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.137552 restraints weight = 17054.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.138240 restraints weight = 12992.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.139639 restraints weight = 11472.832| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25536 Z= 0.183 Angle : 0.746 12.527 34782 Z= 0.395 Chirality : 0.049 0.222 3930 Planarity : 0.005 0.060 4497 Dihedral : 6.817 56.020 3436 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.48 % Favored : 88.14 % Rotamer: Outliers : 4.12 % Allowed : 11.57 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.35 (0.14), residues: 3171 helix: 0.94 (0.21), residues: 555 sheet: -2.05 (0.22), residues: 546 loop : -3.44 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 620 TYR 0.017 0.001 TYR C 163 PHE 0.022 0.002 PHE B 262 TRP 0.017 0.001 TRP C 868 HIS 0.008 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00425 (25497) covalent geometry : angle 0.73247 (34704) SS BOND : bond 0.00811 ( 39) SS BOND : angle 3.07317 ( 78) hydrogen bonds : bond 0.04361 ( 779) hydrogen bonds : angle 6.32105 ( 2085) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 353 time to evaluate : 0.950 Fit side-chains REVERT: A 214 ASN cc_start: 0.8039 (t0) cc_final: 0.7693 (t0) REVERT: A 263 MET cc_start: 0.7928 (ttp) cc_final: 0.7639 (tmm) REVERT: A 454 ASP cc_start: 0.7206 (m-30) cc_final: 0.6691 (p0) REVERT: A 483 PHE cc_start: 0.7525 (m-10) cc_final: 0.7138 (m-80) REVERT: A 499 LEU cc_start: 0.8590 (mm) cc_final: 0.8322 (mm) REVERT: A 577 SER cc_start: 0.8912 (t) cc_final: 0.8707 (m) REVERT: A 605 ASP cc_start: 0.7000 (t70) cc_final: 0.6519 (t0) REVERT: A 641 HIS cc_start: 0.8125 (OUTLIER) cc_final: 0.7890 (t-90) REVERT: A 898 LEU cc_start: 0.6832 (tp) cc_final: 0.6253 (tp) REVERT: A 1011 MET cc_start: 0.9053 (tpp) cc_final: 0.8755 (tpp) REVERT: B 131 GLU cc_start: 0.6784 (tt0) cc_final: 0.6571 (tp30) REVERT: B 184 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7369 (mt-10) REVERT: B 214 ASN cc_start: 0.7636 (t0) cc_final: 0.6880 (t0) REVERT: B 387 PHE cc_start: 0.8179 (p90) cc_final: 0.7933 (p90) REVERT: B 417 MET cc_start: 0.3520 (mmm) cc_final: 0.3110 (mmm) REVERT: B 454 ASP cc_start: 0.7188 (m-30) cc_final: 0.6702 (p0) REVERT: B 621 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8009 (pt) REVERT: B 841 THR cc_start: 0.8646 (t) cc_final: 0.8427 (m) REVERT: B 846 LEU cc_start: 0.8427 (tp) cc_final: 0.8130 (tt) REVERT: B 882 MET cc_start: 0.8019 (mtp) cc_final: 0.7797 (mtp) REVERT: C 184 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7219 (mt-10) REVERT: C 214 ASN cc_start: 0.7550 (t0) cc_final: 0.7194 (t0) REVERT: C 387 PHE cc_start: 0.7997 (p90) cc_final: 0.7730 (p90) REVERT: C 454 ASP cc_start: 0.7062 (m-30) cc_final: 0.6558 (p0) REVERT: C 523 GLN cc_start: 0.8359 (tt0) cc_final: 0.7811 (tt0) REVERT: C 797 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6945 (mtp180) REVERT: C 846 LEU cc_start: 0.8410 (tp) cc_final: 0.8158 (tt) REVERT: C 882 MET cc_start: 0.7498 (mtp) cc_final: 0.7207 (mtp) REVERT: C 898 LEU cc_start: 0.6811 (tp) cc_final: 0.6441 (mt) REVERT: C 1011 MET cc_start: 0.9075 (tpp) cc_final: 0.8841 (tpp) REVERT: C 1019 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.7944 (p) outliers start: 114 outliers final: 81 residues processed: 442 average time/residue: 0.1586 time to fit residues: 114.4678 Evaluate side-chains 374 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 289 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1057 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 768 LYS Chi-restraints excluded: chain C residue 779 PHE Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1012 SER Chi-restraints excluded: chain C residue 1019 SER Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 230 optimal weight: 10.0000 chunk 308 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 314 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 112 GLN A 321 ASN A 409 ASN A 627 ASN A 721 ASN A 883 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 304 ASN B 321 ASN B 409 ASN B 737 GLN C 766 GLN C 896 ASN C 987 GLN C1101 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.179341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.143367 restraints weight = 39348.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.143066 restraints weight = 28167.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.144466 restraints weight = 23549.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.145605 restraints weight = 17339.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.145876 restraints weight = 15259.414| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 25536 Z= 0.194 Angle : 0.729 10.607 34782 Z= 0.386 Chirality : 0.049 0.183 3930 Planarity : 0.005 0.062 4497 Dihedral : 6.636 51.638 3436 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.09 % Favored : 86.47 % Rotamer: Outliers : 4.45 % Allowed : 13.16 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.16 (0.14), residues: 3171 helix: 1.51 (0.22), residues: 537 sheet: -1.91 (0.22), residues: 546 loop : -3.41 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 183 TYR 0.016 0.002 TYR B 440 PHE 0.024 0.002 PHE B 361 TRP 0.022 0.001 TRP C 868 HIS 0.008 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00453 (25497) covalent geometry : angle 0.71871 (34704) SS BOND : bond 0.00775 ( 39) SS BOND : angle 2.66652 ( 78) hydrogen bonds : bond 0.04207 ( 779) hydrogen bonds : angle 6.13601 ( 2085) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 325 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 214 ASN cc_start: 0.7687 (t0) cc_final: 0.7460 (t0) REVERT: A 379 PHE cc_start: 0.6526 (m-10) cc_final: 0.6217 (m-80) REVERT: A 483 PHE cc_start: 0.7448 (m-10) cc_final: 0.7199 (m-80) REVERT: A 499 LEU cc_start: 0.8854 (mm) cc_final: 0.8566 (mm) REVERT: A 1011 MET cc_start: 0.8924 (tpp) cc_final: 0.8572 (tpp) REVERT: B 214 ASN cc_start: 0.7421 (t0) cc_final: 0.6755 (t0) REVERT: B 417 MET cc_start: 0.3722 (mmm) cc_final: 0.3253 (mmm) REVERT: B 454 ASP cc_start: 0.7148 (m-30) cc_final: 0.6877 (p0) REVERT: B 621 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8094 (pt) REVERT: B 841 THR cc_start: 0.8709 (t) cc_final: 0.8495 (m) REVERT: B 888 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: B 965 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7828 (ptt-90) REVERT: C 214 ASN cc_start: 0.7402 (t0) cc_final: 0.7129 (t0) REVERT: C 438 TYR cc_start: 0.6797 (m-80) cc_final: 0.6561 (m-10) REVERT: C 797 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6021 (mtt180) REVERT: C 846 LEU cc_start: 0.8586 (tp) cc_final: 0.8276 (tt) REVERT: C 882 MET cc_start: 0.7489 (mtp) cc_final: 0.7211 (mtp) REVERT: C 1019 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.7984 (p) outliers start: 123 outliers final: 91 residues processed: 418 average time/residue: 0.1532 time to fit residues: 106.3804 Evaluate side-chains 386 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 290 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 883 GLN Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 965 ARG Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1057 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 768 LYS Chi-restraints excluded: chain C residue 779 PHE Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1012 SER Chi-restraints excluded: chain C residue 1019 SER Chi-restraints excluded: chain C residue 1057 PHE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 298 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 221 optimal weight: 0.5980 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 124 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 104 optimal weight: 0.0970 chunk 105 optimal weight: 10.0000 chunk 305 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN C 409 ASN C 737 GLN C 766 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.183368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.148267 restraints weight = 39241.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.148708 restraints weight = 27385.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.150140 restraints weight = 21682.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.150703 restraints weight = 16425.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.151064 restraints weight = 14983.498| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25536 Z= 0.133 Angle : 0.678 10.303 34782 Z= 0.358 Chirality : 0.047 0.178 3930 Planarity : 0.005 0.062 4497 Dihedral : 6.260 50.897 3436 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.26 % Favored : 88.43 % Rotamer: Outliers : 3.69 % Allowed : 14.32 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.87 (0.14), residues: 3171 helix: 1.95 (0.22), residues: 534 sheet: -1.84 (0.22), residues: 552 loop : -3.24 (0.12), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 887 TYR 0.023 0.001 TYR B 689 PHE 0.021 0.001 PHE B 262 TRP 0.025 0.001 TRP C 868 HIS 0.005 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00299 (25497) covalent geometry : angle 0.66708 (34704) SS BOND : bond 0.00665 ( 39) SS BOND : angle 2.61330 ( 78) hydrogen bonds : bond 0.03831 ( 779) hydrogen bonds : angle 5.89873 ( 2085) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 356 time to evaluate : 0.977 Fit side-chains REVERT: A 338 TYR cc_start: 0.5860 (p90) cc_final: 0.5588 (p90) REVERT: A 387 PHE cc_start: 0.7876 (p90) cc_final: 0.7313 (p90) REVERT: A 417 MET cc_start: 0.5078 (mmm) cc_final: 0.4861 (tpp) REVERT: A 499 LEU cc_start: 0.8737 (mm) cc_final: 0.8513 (mm) REVERT: A 841 THR cc_start: 0.8291 (t) cc_final: 0.8029 (m) REVERT: A 1011 MET cc_start: 0.8883 (tpp) cc_final: 0.8544 (tpp) REVERT: B 214 ASN cc_start: 0.7495 (t0) cc_final: 0.7285 (t0) REVERT: B 417 MET cc_start: 0.3810 (mmm) cc_final: 0.3304 (mmm) REVERT: B 621 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8100 (pt) REVERT: B 841 THR cc_start: 0.8664 (t) cc_final: 0.8437 (m) REVERT: B 888 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.7091 (m-80) REVERT: B 948 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8437 (mt) REVERT: B 965 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7267 (ptt-90) REVERT: C 184 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6751 (mt-10) REVERT: C 214 ASN cc_start: 0.7328 (t0) cc_final: 0.7072 (t0) REVERT: C 231 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7495 (p90) REVERT: C 285 GLU cc_start: 0.7503 (tm-30) cc_final: 0.6878 (tm-30) REVERT: C 438 TYR cc_start: 0.6754 (m-80) cc_final: 0.6490 (m-10) REVERT: C 841 THR cc_start: 0.8520 (t) cc_final: 0.8224 (m) REVERT: C 948 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8604 (mt) REVERT: C 965 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7728 (ptp90) outliers start: 102 outliers final: 68 residues processed: 430 average time/residue: 0.1553 time to fit residues: 110.8864 Evaluate side-chains 376 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 301 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 965 ARG Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1057 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 779 PHE Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 965 ARG Chi-restraints excluded: chain C residue 1057 PHE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 209 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN ** B1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN C 759 ASN C 766 GLN C 883 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.184561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.150545 restraints weight = 40321.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.150820 restraints weight = 30841.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.153195 restraints weight = 25492.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.153286 restraints weight = 19007.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.153490 restraints weight = 16844.980| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 25536 Z= 0.221 Angle : 0.741 10.545 34782 Z= 0.390 Chirality : 0.049 0.283 3930 Planarity : 0.005 0.064 4497 Dihedral : 6.382 48.521 3432 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.75 % Favored : 85.97 % Rotamer: Outliers : 4.27 % Allowed : 14.86 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.96 (0.14), residues: 3171 helix: 1.71 (0.22), residues: 537 sheet: -1.79 (0.21), residues: 579 loop : -3.30 (0.12), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.019 0.002 TYR C 677 PHE 0.037 0.002 PHE B 361 TRP 0.025 0.002 TRP C 868 HIS 0.010 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00519 (25497) covalent geometry : angle 0.72875 (34704) SS BOND : bond 0.00749 ( 39) SS BOND : angle 2.93478 ( 78) hydrogen bonds : bond 0.04266 ( 779) hydrogen bonds : angle 5.96009 ( 2085) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 301 time to evaluate : 0.885 Fit side-chains REVERT: A 338 TYR cc_start: 0.6085 (p90) cc_final: 0.5783 (p90) REVERT: A 387 PHE cc_start: 0.7636 (p90) cc_final: 0.7328 (p90) REVERT: A 840 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 1011 MET cc_start: 0.8763 (tpp) cc_final: 0.8426 (tpp) REVERT: B 214 ASN cc_start: 0.7421 (t0) cc_final: 0.7211 (t0) REVERT: B 417 MET cc_start: 0.4013 (mmm) cc_final: 0.3574 (mmm) REVERT: B 545 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7999 (t80) REVERT: B 621 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8216 (pt) REVERT: B 841 THR cc_start: 0.8765 (t) cc_final: 0.8543 (m) REVERT: B 948 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8544 (mt) REVERT: B 965 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7264 (ptt-90) REVERT: C 214 ASN cc_start: 0.7259 (t0) cc_final: 0.7015 (t0) REVERT: C 231 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7655 (p90) REVERT: C 438 TYR cc_start: 0.6766 (m-80) cc_final: 0.6501 (m-10) REVERT: C 483 PHE cc_start: 0.5468 (m-80) cc_final: 0.4790 (m-80) REVERT: C 545 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.6791 (m-80) outliers start: 118 outliers final: 94 residues processed: 391 average time/residue: 0.1550 time to fit residues: 100.8294 Evaluate side-chains 386 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 285 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 149 HIS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 965 ARG Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1057 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 779 PHE Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1012 SER Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 93 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 266 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN C 96 ASN C 766 GLN C 883 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.185878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.152530 restraints weight = 40435.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.153588 restraints weight = 28174.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.154575 restraints weight = 24224.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.155044 restraints weight = 19203.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.155290 restraints weight = 16959.707| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 25536 Z= 0.179 Angle : 0.704 9.653 34782 Z= 0.371 Chirality : 0.048 0.232 3930 Planarity : 0.005 0.057 4497 Dihedral : 6.234 48.971 3432 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.76 % Favored : 87.95 % Rotamer: Outliers : 4.45 % Allowed : 15.47 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.86 (0.14), residues: 3171 helix: 1.86 (0.22), residues: 531 sheet: -1.77 (0.21), residues: 600 loop : -3.22 (0.12), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.025 0.001 TYR C 677 PHE 0.024 0.002 PHE A 262 TRP 0.030 0.002 TRP C 868 HIS 0.008 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00424 (25497) covalent geometry : angle 0.69291 (34704) SS BOND : bond 0.00686 ( 39) SS BOND : angle 2.72846 ( 78) hydrogen bonds : bond 0.04077 ( 779) hydrogen bonds : angle 5.85975 ( 2085) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 308 time to evaluate : 0.961 Fit side-chains REVERT: A 107 MET cc_start: 0.6425 (mmm) cc_final: 0.6186 (mmm) REVERT: A 387 PHE cc_start: 0.7640 (p90) cc_final: 0.7348 (p90) REVERT: A 545 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.6861 (m-80) REVERT: A 691 ASN cc_start: 0.3285 (OUTLIER) cc_final: 0.3060 (p0) REVERT: A 1011 MET cc_start: 0.8790 (tpp) cc_final: 0.8525 (tpp) REVERT: B 96 ASN cc_start: 0.7398 (m-40) cc_final: 0.7186 (m-40) REVERT: B 214 ASN cc_start: 0.7401 (t0) cc_final: 0.7193 (t0) REVERT: B 545 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7932 (t80) REVERT: B 621 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8162 (pt) REVERT: B 841 THR cc_start: 0.8762 (t) cc_final: 0.8480 (m) REVERT: B 948 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8374 (mt) REVERT: C 96 ASN cc_start: 0.7134 (m-40) cc_final: 0.6693 (m-40) REVERT: C 214 ASN cc_start: 0.7137 (t0) cc_final: 0.6928 (t0) REVERT: C 231 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7578 (p90) REVERT: C 387 PHE cc_start: 0.7646 (p90) cc_final: 0.7227 (p90) REVERT: C 438 TYR cc_start: 0.6711 (m-80) cc_final: 0.6454 (m-10) REVERT: C 483 PHE cc_start: 0.5415 (m-80) cc_final: 0.4716 (m-80) REVERT: C 652 ILE cc_start: 0.8490 (tp) cc_final: 0.8273 (tp) REVERT: C 894 THR cc_start: 0.6715 (t) cc_final: 0.6402 (t) outliers start: 123 outliers final: 97 residues processed: 399 average time/residue: 0.1557 time to fit residues: 103.2198 Evaluate side-chains 389 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 286 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 627 ASN Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 494 TYR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1057 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 768 LYS Chi-restraints excluded: chain C residue 779 PHE Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1057 PHE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 258 optimal weight: 0.2980 chunk 304 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 314 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 97 optimal weight: 0.0030 chunk 87 optimal weight: 1.9990 chunk 175 optimal weight: 0.0170 chunk 256 optimal weight: 10.0000 overall best weight: 0.4230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN A 917 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 937 ASN C 505 ASN C 737 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.189642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.156826 restraints weight = 40749.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.157200 restraints weight = 30211.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.159522 restraints weight = 24242.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.159523 restraints weight = 18968.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.159980 restraints weight = 16079.641| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25536 Z= 0.128 Angle : 0.673 11.156 34782 Z= 0.353 Chirality : 0.046 0.227 3930 Planarity : 0.004 0.052 4497 Dihedral : 5.969 48.345 3432 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.94 % Favored : 88.87 % Rotamer: Outliers : 3.40 % Allowed : 17.10 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.64 (0.15), residues: 3171 helix: 1.97 (0.22), residues: 546 sheet: -1.48 (0.22), residues: 555 loop : -3.12 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 758 TYR 0.021 0.001 TYR C 677 PHE 0.025 0.001 PHE B 361 TRP 0.036 0.001 TRP C 868 HIS 0.004 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00292 (25497) covalent geometry : angle 0.66296 (34704) SS BOND : bond 0.00675 ( 39) SS BOND : angle 2.58242 ( 78) hydrogen bonds : bond 0.03697 ( 779) hydrogen bonds : angle 5.69932 ( 2085) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 332 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 107 MET cc_start: 0.6381 (mmm) cc_final: 0.6166 (mmm) REVERT: A 417 MET cc_start: 0.4649 (mmm) cc_final: 0.4268 (tpp) REVERT: A 545 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.6769 (m-80) REVERT: A 841 THR cc_start: 0.8237 (t) cc_final: 0.7942 (m) REVERT: B 96 ASN cc_start: 0.7297 (m-40) cc_final: 0.7052 (m-40) REVERT: B 340 TRP cc_start: 0.5915 (p-90) cc_final: 0.5159 (p-90) REVERT: B 841 THR cc_start: 0.8709 (t) cc_final: 0.8491 (m) REVERT: B 948 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8074 (mt) REVERT: C 231 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7392 (p90) REVERT: C 387 PHE cc_start: 0.7655 (p90) cc_final: 0.7203 (p90) REVERT: C 438 TYR cc_start: 0.6571 (m-80) cc_final: 0.6326 (m-10) REVERT: C 526 ASN cc_start: 0.7027 (t0) cc_final: 0.6779 (t0) REVERT: C 545 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.6395 (m-80) REVERT: C 841 THR cc_start: 0.8517 (t) cc_final: 0.8208 (m) REVERT: C 894 THR cc_start: 0.6598 (t) cc_final: 0.6370 (t) REVERT: C 1011 MET cc_start: 0.8850 (tpp) cc_final: 0.8462 (tpp) outliers start: 94 outliers final: 74 residues processed: 399 average time/residue: 0.1505 time to fit residues: 100.6889 Evaluate side-chains 382 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 304 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 149 HIS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 494 TYR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1057 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 779 PHE Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 1057 PHE Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 265 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 62 optimal weight: 0.0060 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 GLN C 737 GLN C 993 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.187739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.154476 restraints weight = 40424.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.156181 restraints weight = 28428.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.157255 restraints weight = 23418.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.157434 restraints weight = 17009.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.157692 restraints weight = 15518.906| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25536 Z= 0.159 Angle : 0.697 11.881 34782 Z= 0.363 Chirality : 0.047 0.367 3930 Planarity : 0.005 0.061 4497 Dihedral : 5.983 46.923 3432 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.92 % Favored : 87.89 % Rotamer: Outliers : 3.58 % Allowed : 17.17 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.57 (0.15), residues: 3171 helix: 2.09 (0.22), residues: 528 sheet: -1.34 (0.23), residues: 522 loop : -3.07 (0.12), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 758 TYR 0.029 0.001 TYR C 677 PHE 0.027 0.001 PHE A 262 TRP 0.034 0.002 TRP C 868 HIS 0.006 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00375 (25497) covalent geometry : angle 0.68652 (34704) SS BOND : bond 0.00639 ( 39) SS BOND : angle 2.68123 ( 78) hydrogen bonds : bond 0.03863 ( 779) hydrogen bonds : angle 5.68380 ( 2085) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 305 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 483 PHE cc_start: 0.5618 (m-80) cc_final: 0.5303 (m-80) REVERT: A 545 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.6831 (m-80) REVERT: A 841 THR cc_start: 0.8292 (t) cc_final: 0.7970 (m) REVERT: B 96 ASN cc_start: 0.7419 (m-40) cc_final: 0.7205 (m-40) REVERT: B 387 PHE cc_start: 0.7525 (p90) cc_final: 0.7127 (p90) REVERT: B 410 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.6495 (m-10) REVERT: B 841 THR cc_start: 0.8712 (t) cc_final: 0.8448 (m) REVERT: B 882 MET cc_start: 0.7821 (mtp) cc_final: 0.7456 (mtm) REVERT: B 948 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8102 (mt) REVERT: C 231 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7341 (p90) REVERT: C 387 PHE cc_start: 0.7653 (p90) cc_final: 0.7218 (p90) REVERT: C 438 TYR cc_start: 0.6474 (m-80) cc_final: 0.6233 (m-10) REVERT: C 545 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.6657 (m-80) REVERT: C 894 THR cc_start: 0.6990 (t) cc_final: 0.6785 (m) REVERT: C 1011 MET cc_start: 0.8741 (tpp) cc_final: 0.8436 (tpp) outliers start: 99 outliers final: 84 residues processed: 378 average time/residue: 0.1520 time to fit residues: 96.0966 Evaluate side-chains 380 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 291 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 149 HIS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 410 TYR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 494 TYR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1057 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 779 PHE Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 1057 PHE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 68 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 84 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 299 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 264 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN C 737 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.189171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.156104 restraints weight = 40517.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.157543 restraints weight = 27069.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.158422 restraints weight = 22427.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.158931 restraints weight = 17412.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.159068 restraints weight = 15721.599| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25536 Z= 0.138 Angle : 0.690 12.923 34782 Z= 0.358 Chirality : 0.047 0.268 3930 Planarity : 0.004 0.056 4497 Dihedral : 5.882 46.712 3432 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.23 % Favored : 88.58 % Rotamer: Outliers : 3.36 % Allowed : 17.53 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.50 (0.15), residues: 3171 helix: 2.09 (0.22), residues: 528 sheet: -1.23 (0.23), residues: 525 loop : -3.01 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 758 TYR 0.030 0.001 TYR C 677 PHE 0.027 0.001 PHE A 262 TRP 0.038 0.001 TRP C 868 HIS 0.005 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00322 (25497) covalent geometry : angle 0.67977 (34704) SS BOND : bond 0.00624 ( 39) SS BOND : angle 2.56554 ( 78) hydrogen bonds : bond 0.03753 ( 779) hydrogen bonds : angle 5.62450 ( 2085) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 305 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 483 PHE cc_start: 0.5592 (m-80) cc_final: 0.5282 (m-80) REVERT: A 545 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.6806 (m-80) REVERT: A 966 LEU cc_start: 0.8090 (mt) cc_final: 0.7595 (mm) REVERT: B 387 PHE cc_start: 0.7454 (p90) cc_final: 0.6901 (p90) REVERT: B 410 TYR cc_start: 0.6541 (OUTLIER) cc_final: 0.5837 (m-10) REVERT: B 841 THR cc_start: 0.8695 (t) cc_final: 0.8431 (m) REVERT: B 948 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8054 (mt) REVERT: C 231 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7313 (p90) REVERT: C 387 PHE cc_start: 0.7625 (p90) cc_final: 0.7143 (p90) REVERT: C 438 TYR cc_start: 0.6432 (m-80) cc_final: 0.6216 (m-10) REVERT: C 545 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.6631 (m-80) REVERT: C 894 THR cc_start: 0.7366 (t) cc_final: 0.7061 (t) REVERT: C 1011 MET cc_start: 0.8732 (tpp) cc_final: 0.8411 (tpp) outliers start: 93 outliers final: 80 residues processed: 374 average time/residue: 0.1473 time to fit residues: 92.8581 Evaluate side-chains 372 residues out of total 2766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 287 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 149 HIS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 410 TYR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1057 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 527 PHE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 779 PHE Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 1057 PHE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 97 optimal weight: 0.0040 chunk 161 optimal weight: 0.7980 chunk 208 optimal weight: 0.7980 chunk 90 optimal weight: 0.0770 chunk 205 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 255 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.5150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.191013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.158598 restraints weight = 40338.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.160240 restraints weight = 27590.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.161607 restraints weight = 22793.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.161716 restraints weight = 16637.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.162199 restraints weight = 15200.055| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25536 Z= 0.127 Angle : 0.679 12.991 34782 Z= 0.352 Chirality : 0.046 0.241 3930 Planarity : 0.004 0.051 4497 Dihedral : 5.734 46.733 3432 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.79 % Favored : 89.03 % Rotamer: Outliers : 3.04 % Allowed : 18.08 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.44 (0.15), residues: 3171 helix: 2.07 (0.22), residues: 546 sheet: -1.23 (0.23), residues: 513 loop : -2.98 (0.12), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 758 TYR 0.029 0.001 TYR C 677 PHE 0.021 0.001 PHE B 483 TRP 0.038 0.002 TRP C 868 HIS 0.005 0.001 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00293 (25497) covalent geometry : angle 0.66956 (34704) SS BOND : bond 0.00607 ( 39) SS BOND : angle 2.46099 ( 78) hydrogen bonds : bond 0.03611 ( 779) hydrogen bonds : angle 5.52978 ( 2085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4036.29 seconds wall clock time: 70 minutes 48.34 seconds (4248.34 seconds total)