Starting phenix.real_space_refine on Wed Nov 19 11:56:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xlr_6732/11_2025/5xlr_6732.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xlr_6732/11_2025/5xlr_6732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5xlr_6732/11_2025/5xlr_6732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xlr_6732/11_2025/5xlr_6732.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5xlr_6732/11_2025/5xlr_6732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xlr_6732/11_2025/5xlr_6732.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 132 5.16 5 C 15279 2.51 5 N 3954 2.21 5 O 4536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 23901 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7967 Classifications: {'peptide': 1022} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 6 Restraints were copied for chains: B, C Time building chain proxies: 9.28, per 1000 atoms: 0.39 Number of scatterers: 23901 At special positions: 0 Unit cell: (132, 133.32, 163.68, 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 132 16.00 O 4536 8.00 N 3954 7.00 C 15279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.02 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " 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=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.02 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.02 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.02 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.02 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5736 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 39 sheets defined 23.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 267 through 271 removed outlier: 4.059A pdb=" N THR A 271 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.513A pdb=" N LYS A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 390 through 397 removed outlier: 4.215A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 603 through 611 Processing helix chain 'A' and resid 729 through 739 removed outlier: 3.503A pdb=" N GLY A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.809A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 810 Processing helix chain 'A' and resid 815 through 820 removed outlier: 4.197A pdb=" N TYR A 819 " --> pdb=" O PHE A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 865 Processing helix chain 'A' and resid 879 through 892 Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.541A pdb=" N ASN A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 920 Processing helix chain 'A' and resid 927 through 949 removed outlier: 3.665A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 949 " --> pdb=" O VAL A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 971 through 1015 removed outlier: 4.020A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 982 " --> pdb=" O LEU A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'B' and resid 267 through 271 removed outlier: 4.059A pdb=" N THR B 271 " --> pdb=" O GLU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.512A pdb=" N LYS B 291 " --> pdb=" O LYS B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 390 through 397 removed outlier: 4.214A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 603 through 611 Processing helix chain 'B' and resid 729 through 739 removed outlier: 3.505A pdb=" N GLY B 739 " --> pdb=" O LEU B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 765 removed outlier: 3.811A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 810 Processing helix chain 'B' and resid 815 through 820 removed outlier: 4.197A pdb=" N TYR B 819 " --> pdb=" O PHE B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 865 Processing helix chain 'B' and resid 879 through 892 Processing helix chain 'B' and resid 895 through 901 removed outlier: 3.540A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 920 Processing helix chain 'B' and resid 927 through 949 removed outlier: 3.665A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 949 " --> pdb=" O VAL B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 971 through 1015 removed outlier: 4.019A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 982 " --> pdb=" O LEU B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'C' and resid 267 through 271 removed outlier: 4.059A pdb=" N THR C 271 " --> pdb=" O GLU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.513A pdb=" N LYS C 291 " --> pdb=" O LYS C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 390 through 397 removed outlier: 4.214A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 603 through 611 Processing helix chain 'C' and resid 729 through 739 removed outlier: 3.504A pdb=" N GLY C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.810A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 810 Processing helix chain 'C' and resid 815 through 820 removed outlier: 4.197A pdb=" N TYR C 819 " --> pdb=" O PHE C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 865 Processing helix chain 'C' and resid 879 through 892 Processing helix chain 'C' and resid 895 through 901 removed outlier: 3.541A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 920 Processing helix chain 'C' and resid 927 through 949 removed outlier: 3.665A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 971 through 1015 removed outlier: 4.019A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C 982 " --> pdb=" O LEU C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1102 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 removed outlier: 7.145A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 166 Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 306 removed outlier: 3.859A pdb=" N GLY A 298 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR A 585 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 3.625A pdb=" N GLY A 311 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 537 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 570 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 345 removed outlier: 5.031A pdb=" N ASN A 381 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU A 502 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AA8, first strand: chain 'A' and resid 650 through 652 Processing sheet with id=AA9, first strand: chain 'A' and resid 694 through 696 Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 710 Processing sheet with id=AB2, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB3, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 3.582A pdb=" N ILE A1063 " --> pdb=" O TYR A1070 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1077 through 1079 Processing sheet with id=AB5, first strand: chain 'B' and resid 34 through 36 removed outlier: 7.145A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 55 Processing sheet with id=AB7, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AB8, first strand: chain 'B' and resid 298 through 306 removed outlier: 3.859A pdb=" N GLY B 298 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR B 585 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 315 removed outlier: 3.625A pdb=" N GLY B 311 " --> pdb=" O CYS B 524 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 537 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 570 " --> pdb=" O VAL B 562 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 341 through 345 removed outlier: 5.030A pdb=" N ASN B 381 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU B 502 " --> pdb=" O ASN B 381 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AC3, first strand: chain 'B' and resid 650 through 652 Processing sheet with id=AC4, first strand: chain 'B' and resid 694 through 696 Processing sheet with id=AC5, first strand: chain 'B' and resid 701 through 710 Processing sheet with id=AC6, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AC7, first strand: chain 'B' and resid 1063 through 1064 removed outlier: 3.582A pdb=" N ILE B1063 " --> pdb=" O TYR B1070 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1077 through 1079 Processing sheet with id=AC9, first strand: chain 'C' and resid 34 through 36 removed outlier: 7.145A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 51 through 55 Processing sheet with id=AD2, first strand: chain 'C' and resid 164 through 166 Processing sheet with id=AD3, first strand: chain 'C' and resid 298 through 306 removed outlier: 3.857A pdb=" N GLY C 298 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR C 585 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 315 removed outlier: 3.625A pdb=" N GLY C 311 " --> pdb=" O CYS C 524 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 537 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 570 " --> pdb=" O VAL C 562 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 341 through 345 removed outlier: 5.030A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU C 502 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AD7, first strand: chain 'C' and resid 650 through 652 Processing sheet with id=AD8, first strand: chain 'C' and resid 694 through 696 Processing sheet with id=AD9, first strand: chain 'C' and resid 701 through 710 Processing sheet with id=AE1, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AE2, first strand: chain 'C' and resid 1063 through 1064 removed outlier: 3.582A pdb=" N ILE C1063 " --> pdb=" O TYR C1070 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1077 through 1079 894 hydrogen bonds defined for protein. 2358 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: 5.51 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7555 1.34 - 1.46: 5559 1.46 - 1.58: 11159 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 24453 Sorted by residual: bond pdb=" C LYS B 411 " pdb=" N LEU B 412 " ideal model delta sigma weight residual 1.331 1.239 0.091 3.12e-02 1.03e+03 8.59e+00 bond pdb=" C LYS C 411 " pdb=" N LEU C 412 " ideal model delta sigma weight residual 1.331 1.239 0.091 3.12e-02 1.03e+03 8.59e+00 bond pdb=" C LYS A 411 " pdb=" N LEU A 412 " ideal model delta sigma weight residual 1.331 1.239 0.091 3.12e-02 1.03e+03 8.58e+00 bond pdb=" C ILE B 787 " pdb=" N LEU B 788 " ideal model delta sigma weight residual 1.331 1.251 0.080 2.83e-02 1.25e+03 7.90e+00 bond pdb=" C LEU A1031 " pdb=" N MET A1032 " ideal model delta sigma weight residual 1.330 1.355 -0.025 1.19e-02 7.06e+03 4.30e+00 ... (remaining 24448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 31604 2.44 - 4.87: 1386 4.87 - 7.31: 217 7.31 - 9.75: 36 9.75 - 12.18: 12 Bond angle restraints: 33255 Sorted by residual: angle pdb=" N ASN A 227 " pdb=" CA ASN A 227 " pdb=" C ASN A 227 " ideal model delta sigma weight residual 107.73 115.58 -7.85 1.34e+00 5.57e-01 3.43e+01 angle pdb=" N ASN B 227 " pdb=" CA ASN B 227 " pdb=" C ASN B 227 " ideal model delta sigma weight residual 107.73 115.58 -7.85 1.34e+00 5.57e-01 3.43e+01 angle pdb=" N ASN C 227 " pdb=" CA ASN C 227 " pdb=" C ASN C 227 " ideal model delta sigma weight residual 107.73 115.56 -7.83 1.34e+00 5.57e-01 3.42e+01 angle pdb=" C LYS A 566 " pdb=" N THR A 567 " pdb=" CA THR A 567 " ideal model delta sigma weight residual 122.78 130.94 -8.16 1.52e+00 4.33e-01 2.88e+01 angle pdb=" C LYS C 566 " pdb=" N THR C 567 " pdb=" CA THR C 567 " ideal model delta sigma weight residual 122.78 130.91 -8.13 1.52e+00 4.33e-01 2.86e+01 ... (remaining 33250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 13700 16.27 - 32.55: 719 32.55 - 48.82: 122 48.82 - 65.09: 12 65.09 - 81.36: 6 Dihedral angle restraints: 14559 sinusoidal: 5634 harmonic: 8925 Sorted by residual: dihedral pdb=" CA ILE B 573 " pdb=" C ILE B 573 " pdb=" N SER B 574 " pdb=" CA SER B 574 " ideal model delta harmonic sigma weight residual -180.00 -132.44 -47.56 0 5.00e+00 4.00e-02 9.05e+01 dihedral pdb=" CA ILE C 573 " pdb=" C ILE C 573 " pdb=" N SER C 574 " pdb=" CA SER C 574 " ideal model delta harmonic sigma weight residual -180.00 -132.49 -47.51 0 5.00e+00 4.00e-02 9.03e+01 dihedral pdb=" CA ILE A 573 " pdb=" C ILE A 573 " pdb=" N SER A 574 " pdb=" CA SER A 574 " ideal model delta harmonic sigma weight residual -180.00 -132.51 -47.49 0 5.00e+00 4.00e-02 9.02e+01 ... (remaining 14556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2522 0.057 - 0.113: 929 0.113 - 0.170: 266 0.170 - 0.227: 39 0.227 - 0.284: 6 Chirality restraints: 3762 Sorted by residual: chirality pdb=" CA THR B 567 " pdb=" N THR B 567 " pdb=" C THR B 567 " pdb=" CB THR B 567 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA THR A 567 " pdb=" N THR A 567 " pdb=" C THR A 567 " pdb=" CB THR A 567 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA THR C 567 " pdb=" N THR C 567 " pdb=" C THR C 567 " pdb=" CB THR C 567 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 3759 not shown) Planarity restraints: 4302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 502 " -0.031 2.00e-02 2.50e+03 6.17e-02 3.81e+01 pdb=" C GLU C 502 " 0.107 2.00e-02 2.50e+03 pdb=" O GLU C 502 " -0.041 2.00e-02 2.50e+03 pdb=" N LEU C 503 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 502 " -0.031 2.00e-02 2.50e+03 6.16e-02 3.79e+01 pdb=" C GLU A 502 " 0.107 2.00e-02 2.50e+03 pdb=" O GLU A 502 " -0.040 2.00e-02 2.50e+03 pdb=" N LEU A 503 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 502 " 0.031 2.00e-02 2.50e+03 6.14e-02 3.77e+01 pdb=" C GLU B 502 " -0.106 2.00e-02 2.50e+03 pdb=" O GLU B 502 " 0.040 2.00e-02 2.50e+03 pdb=" N LEU B 503 " 0.035 2.00e-02 2.50e+03 ... (remaining 4299 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 794 2.69 - 3.24: 22807 3.24 - 3.80: 36940 3.80 - 4.35: 46462 4.35 - 4.90: 77525 Nonbonded interactions: 184528 Sorted by model distance: nonbonded pdb=" NE2 GLN A 549 " pdb=" OE1 GLU C 45 " model vdw 2.139 3.120 nonbonded pdb=" ND2 ASN A 304 " pdb=" OD1 ASP C 719 " model vdw 2.147 3.120 nonbonded pdb=" OD1 ASP A 719 " pdb=" ND2 ASN B 304 " model vdw 2.198 3.120 nonbonded pdb=" O PHE C 805 " pdb=" OG1 THR C 809 " model vdw 2.215 3.040 nonbonded pdb=" O PHE A 805 " pdb=" OG1 THR A 809 " model vdw 2.215 3.040 ... (remaining 184523 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: 1.670 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.300 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 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 : 0.008 0.091 24495 Z= 0.371 Angle : 1.179 12.182 33339 Z= 0.672 Chirality : 0.063 0.284 3762 Planarity : 0.009 0.108 4302 Dihedral : 9.811 55.170 8697 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.30 % Allowed : 14.55 % Favored : 85.15 % Rotamer: Outliers : 0.38 % Allowed : 2.35 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.62 % 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: -4.45 (0.12), residues: 3024 helix: -2.64 (0.13), residues: 699 sheet: -1.59 (0.21), residues: 516 loop : -3.71 (0.12), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 315 TYR 0.030 0.004 TYR B 886 PHE 0.047 0.004 PHE A 193 TRP 0.021 0.002 TRP B 423 HIS 0.021 0.004 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00819 (24453) covalent geometry : angle 1.17081 (33255) SS BOND : bond 0.00468 ( 42) SS BOND : angle 3.02750 ( 84) hydrogen bonds : bond 0.11736 ( 894) hydrogen bonds : angle 10.64314 ( 2358) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 708 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 PHE cc_start: 0.6028 (t80) cc_final: 0.5759 (t80) REVERT: A 216 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5522 (pp) REVERT: A 220 PHE cc_start: 0.5276 (t80) cc_final: 0.4948 (t80) REVERT: A 301 GLN cc_start: 0.8708 (tt0) cc_final: 0.8348 (tm-30) REVERT: A 850 ASP cc_start: 0.8968 (m-30) cc_final: 0.8553 (t0) REVERT: A 884 MET cc_start: 0.6871 (mmm) cc_final: 0.6550 (mmt) REVERT: A 899 TYR cc_start: 0.5974 (t80) cc_final: 0.5646 (t80) REVERT: A 948 LEU cc_start: 0.9482 (tp) cc_final: 0.9262 (tt) REVERT: A 1027 LYS cc_start: 0.8705 (tttt) cc_final: 0.8481 (tppt) REVERT: B 216 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5295 (pp) REVERT: B 220 PHE cc_start: 0.5563 (t80) cc_final: 0.5336 (t80) REVERT: B 301 GLN cc_start: 0.8901 (tt0) cc_final: 0.8642 (tm-30) REVERT: B 405 ILE cc_start: 0.7880 (mm) cc_final: 0.7583 (mp) REVERT: B 850 ASP cc_start: 0.9121 (m-30) cc_final: 0.8817 (p0) REVERT: B 894 THR cc_start: 0.8161 (m) cc_final: 0.7954 (p) REVERT: B 973 VAL cc_start: 0.8782 (p) cc_final: 0.8569 (m) REVERT: C 89 PHE cc_start: 0.6230 (t80) cc_final: 0.5898 (t80) REVERT: C 220 PHE cc_start: 0.5565 (t80) cc_final: 0.5328 (t80) REVERT: C 301 GLN cc_start: 0.8787 (tt0) cc_final: 0.8398 (tm-30) REVERT: C 532 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7085 (tm) REVERT: C 733 ASN cc_start: 0.7955 (m-40) cc_final: 0.7567 (m-40) REVERT: C 850 ASP cc_start: 0.9232 (m-30) cc_final: 0.8700 (t0) REVERT: C 868 TRP cc_start: 0.6833 (p-90) cc_final: 0.6417 (p-90) REVERT: C 973 VAL cc_start: 0.8757 (p) cc_final: 0.8375 (m) outliers start: 10 outliers final: 1 residues processed: 718 average time/residue: 0.1913 time to fit residues: 205.7341 Evaluate side-chains 381 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 377 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 532 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0170 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 149 HIS A 201 GLN A 214 ASN ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 GLN A 883 GLN A 889 ASN A 904 GLN A 931 GLN B 109 ASN B 129 ASN B 149 HIS ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 214 ASN B 769 GLN B 889 ASN B 904 GLN B 984 GLN B1046 HIS C 109 ASN C 149 HIS ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 214 ASN C 769 GLN C 889 ASN C 904 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.133472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.103375 restraints weight = 56879.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.106187 restraints weight = 32561.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.108064 restraints weight = 22143.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.109259 restraints weight = 17013.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.110068 restraints weight = 14282.900| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 24495 Z= 0.169 Angle : 0.819 9.716 33339 Z= 0.430 Chirality : 0.049 0.343 3762 Planarity : 0.007 0.105 4302 Dihedral : 7.527 41.705 3301 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.38 % Favored : 88.53 % Rotamer: Outliers : 2.57 % Allowed : 10.44 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.28 % 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: -3.13 (0.14), residues: 3024 helix: -0.01 (0.19), residues: 687 sheet: -1.05 (0.22), residues: 525 loop : -3.47 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C1089 TYR 0.024 0.002 TYR C 886 PHE 0.042 0.002 PHE C 262 TRP 0.010 0.001 TRP A1084 HIS 0.009 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00386 (24453) covalent geometry : angle 0.80548 (33255) SS BOND : bond 0.00507 ( 42) SS BOND : angle 3.05565 ( 84) hydrogen bonds : bond 0.04488 ( 894) hydrogen bonds : angle 7.53726 ( 2358) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 465 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7687 (ppp) cc_final: 0.7025 (ppp) REVERT: A 89 PHE cc_start: 0.7453 (t80) cc_final: 0.7225 (t80) REVERT: A 101 TRP cc_start: 0.8212 (m100) cc_final: 0.7687 (m100) REVERT: A 216 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6545 (pp) REVERT: A 220 PHE cc_start: 0.6703 (t80) cc_final: 0.6247 (t80) REVERT: A 395 ARG cc_start: 0.7530 (tmm160) cc_final: 0.7329 (tmm160) REVERT: A 441 ARG cc_start: 0.6612 (mtp85) cc_final: 0.6128 (mtp85) REVERT: A 899 TYR cc_start: 0.6001 (t80) cc_final: 0.4660 (t80) REVERT: A 927 LEU cc_start: 0.8836 (mp) cc_final: 0.8605 (tt) REVERT: A 956 SER cc_start: 0.8950 (t) cc_final: 0.8735 (p) REVERT: B 49 SER cc_start: 0.8501 (t) cc_final: 0.8285 (t) REVERT: B 102 VAL cc_start: 0.8447 (t) cc_final: 0.8095 (t) REVERT: B 107 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6381 (mmp) REVERT: B 185 PHE cc_start: 0.8318 (m-80) cc_final: 0.8041 (m-80) REVERT: B 191 ASP cc_start: 0.7912 (t0) cc_final: 0.7308 (t70) REVERT: B 216 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6767 (pp) REVERT: B 346 SER cc_start: 0.8671 (p) cc_final: 0.7812 (m) REVERT: B 405 ILE cc_start: 0.8762 (mm) cc_final: 0.8164 (mp) REVERT: B 440 TYR cc_start: 0.7598 (p90) cc_final: 0.6711 (p90) REVERT: B 441 ARG cc_start: 0.6048 (ttt90) cc_final: 0.5762 (ttm-80) REVERT: B 515 LEU cc_start: 0.8877 (mt) cc_final: 0.8573 (tp) REVERT: B 558 PHE cc_start: 0.7504 (m-80) cc_final: 0.6996 (m-80) REVERT: B 709 MET cc_start: 0.8912 (mtp) cc_final: 0.8653 (mtp) REVERT: B 894 THR cc_start: 0.8393 (m) cc_final: 0.7721 (p) REVERT: B 1011 MET cc_start: 0.8812 (ttm) cc_final: 0.8402 (ttm) REVERT: C 89 PHE cc_start: 0.7337 (t80) cc_final: 0.6992 (t80) REVERT: C 185 PHE cc_start: 0.8552 (m-80) cc_final: 0.7967 (m-10) REVERT: C 220 PHE cc_start: 0.6604 (t80) cc_final: 0.6397 (t80) REVERT: C 224 LEU cc_start: 0.7795 (mt) cc_final: 0.7471 (mt) REVERT: C 257 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7207 (pp) REVERT: C 532 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7574 (tm) REVERT: C 558 PHE cc_start: 0.7701 (m-80) cc_final: 0.7484 (m-80) REVERT: C 1089 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6726 (mtt90) outliers start: 68 outliers final: 39 residues processed: 510 average time/residue: 0.1717 time to fit residues: 138.1873 Evaluate side-chains 412 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 367 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 360 PHE Chi-restraints excluded: chain B residue 444 ARG Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 766 GLN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 979 ILE Chi-restraints excluded: chain B residue 1068 LYS Chi-restraints excluded: chain B residue 1087 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 1087 THR Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1092 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 89 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 295 optimal weight: 0.6980 chunk 106 optimal weight: 0.0570 chunk 182 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 181 HIS ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 GLN A 746 ASN A 947 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 ASN B 984 GLN B1046 HIS C 109 ASN ** C 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.134023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.104230 restraints weight = 56359.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107063 restraints weight = 31732.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.108936 restraints weight = 21339.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.110144 restraints weight = 16274.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.110969 restraints weight = 13606.462| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24495 Z= 0.145 Angle : 0.757 19.357 33339 Z= 0.392 Chirality : 0.048 0.240 3762 Planarity : 0.006 0.094 4302 Dihedral : 6.807 36.720 3301 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 2.91 % Allowed : 12.33 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.24 % 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: -2.51 (0.15), residues: 3024 helix: 1.13 (0.20), residues: 669 sheet: -0.77 (0.22), residues: 552 loop : -3.30 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1089 TYR 0.023 0.002 TYR A 886 PHE 0.035 0.002 PHE C 262 TRP 0.022 0.001 TRP C 101 HIS 0.008 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00323 (24453) covalent geometry : angle 0.74923 (33255) SS BOND : bond 0.00698 ( 42) SS BOND : angle 2.21985 ( 84) hydrogen bonds : bond 0.04018 ( 894) hydrogen bonds : angle 6.78227 ( 2358) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 409 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 PHE cc_start: 0.7305 (t80) cc_final: 0.7095 (t80) REVERT: A 101 TRP cc_start: 0.8200 (m100) cc_final: 0.7281 (m-90) REVERT: A 183 ARG cc_start: 0.6384 (mmt180) cc_final: 0.6169 (mmt180) REVERT: A 184 GLU cc_start: 0.6459 (tt0) cc_final: 0.6222 (tt0) REVERT: A 216 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6584 (pp) REVERT: A 220 PHE cc_start: 0.6594 (t80) cc_final: 0.6239 (t80) REVERT: A 558 PHE cc_start: 0.7269 (m-80) cc_final: 0.6710 (m-80) REVERT: A 837 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: A 956 SER cc_start: 0.9087 (t) cc_final: 0.8851 (p) REVERT: B 87 ILE cc_start: 0.9351 (mm) cc_final: 0.9145 (mm) REVERT: B 191 ASP cc_start: 0.7968 (t0) cc_final: 0.7318 (t70) REVERT: B 216 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.5769 (pp) REVERT: B 220 PHE cc_start: 0.6657 (t80) cc_final: 0.6329 (t80) REVERT: B 346 SER cc_start: 0.8658 (p) cc_final: 0.7801 (m) REVERT: B 373 LYS cc_start: 0.8233 (mtpp) cc_final: 0.7976 (mtmt) REVERT: B 405 ILE cc_start: 0.8756 (mm) cc_final: 0.8279 (mp) REVERT: B 440 TYR cc_start: 0.7553 (p90) cc_final: 0.6587 (p90) REVERT: B 558 PHE cc_start: 0.7829 (m-80) cc_final: 0.7247 (m-80) REVERT: B 1011 MET cc_start: 0.8737 (ttm) cc_final: 0.8154 (ttm) REVERT: C 220 PHE cc_start: 0.6571 (t80) cc_final: 0.6275 (t80) REVERT: C 285 GLU cc_start: 0.8781 (tt0) cc_final: 0.8510 (tm-30) REVERT: C 348 CYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7635 (t) REVERT: C 373 LYS cc_start: 0.8246 (mtpp) cc_final: 0.7886 (mtmm) REVERT: C 532 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7634 (tt) REVERT: C 582 SER cc_start: 0.9435 (m) cc_final: 0.9127 (t) REVERT: C 727 ASP cc_start: 0.8336 (p0) cc_final: 0.8115 (p0) REVERT: C 966 LEU cc_start: 0.8851 (mt) cc_final: 0.8470 (mm) outliers start: 77 outliers final: 47 residues processed: 454 average time/residue: 0.1650 time to fit residues: 119.0995 Evaluate side-chains 413 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 361 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 360 PHE Chi-restraints excluded: chain B residue 444 ARG Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 896 ASN Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 979 ILE Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1098 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 153 optimal weight: 0.0470 chunk 76 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 281 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 219 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 overall best weight: 1.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN B 904 GLN B 984 GLN B1046 HIS B1090 ASN ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 181 HIS ** C 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN C 939 GLN C1046 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.129794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.098961 restraints weight = 57425.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.101576 restraints weight = 33843.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.103315 restraints weight = 23469.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.104459 restraints weight = 18292.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.105164 restraints weight = 15520.459| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 24495 Z= 0.225 Angle : 0.810 16.412 33339 Z= 0.416 Chirality : 0.050 0.270 3762 Planarity : 0.006 0.098 4302 Dihedral : 6.775 39.408 3300 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.76 % Favored : 87.14 % Rotamer: Outliers : 3.75 % Allowed : 13.96 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.10 % 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: 3024 helix: 1.25 (0.21), residues: 663 sheet: -0.94 (0.21), residues: 582 loop : -3.22 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1089 TYR 0.025 0.002 TYR A 886 PHE 0.039 0.002 PHE C 262 TRP 0.018 0.001 TRP C 101 HIS 0.007 0.002 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00511 (24453) covalent geometry : angle 0.80091 (33255) SS BOND : bond 0.00756 ( 42) SS BOND : angle 2.60145 ( 84) hydrogen bonds : bond 0.04367 ( 894) hydrogen bonds : angle 6.58045 ( 2358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 371 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6852 (pp) REVERT: A 220 PHE cc_start: 0.6331 (t80) cc_final: 0.5933 (t80) REVERT: A 441 ARG cc_start: 0.6625 (mtp85) cc_final: 0.5827 (mtp85) REVERT: A 558 PHE cc_start: 0.7134 (m-80) cc_final: 0.6858 (m-80) REVERT: A 837 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: B 101 TRP cc_start: 0.8167 (m-90) cc_final: 0.7897 (m100) REVERT: B 191 ASP cc_start: 0.8046 (t0) cc_final: 0.7359 (t70) REVERT: B 216 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6226 (pp) REVERT: B 220 PHE cc_start: 0.6703 (t80) cc_final: 0.6363 (t80) REVERT: B 263 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8374 (ttm) REVERT: B 373 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7905 (mtmt) REVERT: B 405 ILE cc_start: 0.8754 (mm) cc_final: 0.8227 (mp) REVERT: B 440 TYR cc_start: 0.7598 (p90) cc_final: 0.6656 (p90) REVERT: B 558 PHE cc_start: 0.7831 (m-80) cc_final: 0.7233 (m-80) REVERT: B 1011 MET cc_start: 0.8702 (ttm) cc_final: 0.8238 (ttm) REVERT: C 183 ARG cc_start: 0.6060 (mmt180) cc_final: 0.5846 (mmt180) REVERT: C 220 PHE cc_start: 0.6232 (t80) cc_final: 0.5863 (t80) REVERT: C 348 CYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7738 (t) REVERT: C 373 LYS cc_start: 0.8228 (mtpp) cc_final: 0.7776 (mtmm) REVERT: C 532 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7706 (tm) REVERT: C 837 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: C 966 LEU cc_start: 0.8932 (mt) cc_final: 0.8647 (mp) REVERT: C 1013 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7605 (mt-10) outliers start: 99 outliers final: 67 residues processed: 430 average time/residue: 0.1720 time to fit residues: 118.1907 Evaluate side-chains 399 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 325 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 360 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 979 ILE Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 896 ASN Chi-restraints excluded: chain C residue 1087 THR Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1098 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 242 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 0.0030 chunk 37 optimal weight: 0.5980 chunk 295 optimal weight: 0.8980 chunk 173 optimal weight: 0.6980 chunk 249 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 268 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN ** C 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.133421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103425 restraints weight = 57337.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106097 restraints weight = 33671.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107884 restraints weight = 23307.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.109066 restraints weight = 18123.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.109812 restraints weight = 15361.228| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 24495 Z= 0.136 Angle : 0.755 18.947 33339 Z= 0.384 Chirality : 0.047 0.301 3762 Planarity : 0.005 0.105 4302 Dihedral : 6.450 37.266 3300 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.71 % Favored : 88.29 % Rotamer: Outliers : 3.06 % Allowed : 15.66 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.14 % 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: -2.29 (0.15), residues: 3024 helix: 1.45 (0.21), residues: 690 sheet: -0.88 (0.21), residues: 582 loop : -3.22 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1089 TYR 0.030 0.001 TYR B 886 PHE 0.033 0.002 PHE C 262 TRP 0.023 0.001 TRP C 101 HIS 0.005 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00304 (24453) covalent geometry : angle 0.73788 (33255) SS BOND : bond 0.00606 ( 42) SS BOND : angle 3.26199 ( 84) hydrogen bonds : bond 0.03979 ( 894) hydrogen bonds : angle 6.26058 ( 2358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 381 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 ARG cc_start: 0.6585 (mtp85) cc_final: 0.5830 (ttm170) REVERT: A 503 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7799 (mm) REVERT: A 554 ASP cc_start: 0.6270 (t0) cc_final: 0.5728 (t0) REVERT: A 558 PHE cc_start: 0.7182 (m-80) cc_final: 0.6935 (m-80) REVERT: A 735 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8887 (tt) REVERT: A 837 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7649 (m-80) REVERT: B 42 TYR cc_start: 0.5959 (OUTLIER) cc_final: 0.5395 (t80) REVERT: B 191 ASP cc_start: 0.7964 (t0) cc_final: 0.7265 (t70) REVERT: B 257 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6619 (mp) REVERT: B 263 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8352 (ttm) REVERT: B 346 SER cc_start: 0.8716 (p) cc_final: 0.7992 (m) REVERT: B 373 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7782 (mtmt) REVERT: B 405 ILE cc_start: 0.8745 (mm) cc_final: 0.8220 (mp) REVERT: B 440 TYR cc_start: 0.7754 (p90) cc_final: 0.6918 (p90) REVERT: B 558 PHE cc_start: 0.7705 (m-80) cc_final: 0.7148 (m-80) REVERT: B 677 TYR cc_start: 0.8659 (p90) cc_final: 0.8405 (p90) REVERT: B 818 GLN cc_start: 0.7414 (mp10) cc_final: 0.7156 (mp10) REVERT: B 944 LEU cc_start: 0.9245 (tp) cc_final: 0.9029 (tp) REVERT: B 992 GLN cc_start: 0.8606 (mt0) cc_final: 0.8385 (mm-40) REVERT: B 1011 MET cc_start: 0.8655 (ttm) cc_final: 0.8257 (ttm) REVERT: C 197 TYR cc_start: 0.7837 (m-10) cc_final: 0.7579 (m-80) REVERT: C 348 CYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7545 (t) REVERT: C 373 LYS cc_start: 0.8283 (mtpp) cc_final: 0.7948 (mtmm) REVERT: C 441 ARG cc_start: 0.6647 (mtp85) cc_final: 0.6246 (ttm-80) REVERT: C 532 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7817 (tm) REVERT: C 582 SER cc_start: 0.9457 (m) cc_final: 0.9239 (t) REVERT: C 621 ILE cc_start: 0.8648 (mt) cc_final: 0.8415 (pt) REVERT: C 837 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7934 (m-80) REVERT: C 966 LEU cc_start: 0.8927 (mt) cc_final: 0.8517 (mm) outliers start: 81 outliers final: 49 residues processed: 430 average time/residue: 0.1625 time to fit residues: 112.3199 Evaluate side-chains 403 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 345 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 360 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1098 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 122 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 22 optimal weight: 0.4980 chunk 174 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 217 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 82 optimal weight: 0.0030 chunk 193 optimal weight: 0.3980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 ASN A 889 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN C 627 ASN C 744 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.134267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.104374 restraints weight = 56790.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.107165 restraints weight = 32378.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.109014 restraints weight = 21900.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110256 restraints weight = 16762.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.110935 restraints weight = 14036.962| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24495 Z= 0.127 Angle : 0.731 14.842 33339 Z= 0.368 Chirality : 0.047 0.264 3762 Planarity : 0.005 0.096 4302 Dihedral : 6.089 34.886 3296 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 3.25 % Allowed : 16.19 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.17 (0.15), residues: 3024 helix: 1.65 (0.21), residues: 687 sheet: -0.89 (0.21), residues: 600 loop : -3.16 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1089 TYR 0.025 0.001 TYR B 886 PHE 0.037 0.002 PHE A 231 TRP 0.026 0.001 TRP C 101 HIS 0.005 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00282 (24453) covalent geometry : angle 0.71806 (33255) SS BOND : bond 0.00418 ( 42) SS BOND : angle 2.77364 ( 84) hydrogen bonds : bond 0.03757 ( 894) hydrogen bonds : angle 6.05241 ( 2358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 379 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8306 (pttt) cc_final: 0.8082 (ptmm) REVERT: A 441 ARG cc_start: 0.6564 (mtp85) cc_final: 0.5803 (mtp85) REVERT: A 503 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7753 (mm) REVERT: A 554 ASP cc_start: 0.6288 (t0) cc_final: 0.5864 (t0) REVERT: A 558 PHE cc_start: 0.7191 (m-80) cc_final: 0.6950 (m-80) REVERT: A 735 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8840 (tt) REVERT: A 837 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: A 942 ASN cc_start: 0.8619 (m-40) cc_final: 0.8280 (m-40) REVERT: B 42 TYR cc_start: 0.5998 (OUTLIER) cc_final: 0.5023 (t80) REVERT: B 191 ASP cc_start: 0.7823 (t0) cc_final: 0.7254 (t70) REVERT: B 257 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6385 (mp) REVERT: B 263 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8389 (ttm) REVERT: B 346 SER cc_start: 0.8498 (p) cc_final: 0.7785 (m) REVERT: B 405 ILE cc_start: 0.8720 (mm) cc_final: 0.8213 (mp) REVERT: B 440 TYR cc_start: 0.7594 (p90) cc_final: 0.6745 (p90) REVERT: B 558 PHE cc_start: 0.7620 (m-80) cc_final: 0.7078 (m-80) REVERT: B 600 ASP cc_start: 0.7616 (m-30) cc_final: 0.7401 (m-30) REVERT: B 818 GLN cc_start: 0.7280 (mp10) cc_final: 0.7022 (mp10) REVERT: B 944 LEU cc_start: 0.9263 (tp) cc_final: 0.9033 (tp) REVERT: B 966 LEU cc_start: 0.8998 (mm) cc_final: 0.8683 (mm) REVERT: B 1011 MET cc_start: 0.8654 (ttm) cc_final: 0.8429 (ttm) REVERT: B 1073 ARG cc_start: 0.7684 (tmm160) cc_final: 0.7426 (tmm160) REVERT: C 42 TYR cc_start: 0.6371 (OUTLIER) cc_final: 0.4763 (t80) REVERT: C 183 ARG cc_start: 0.6238 (mmt180) cc_final: 0.5848 (mmt180) REVERT: C 348 CYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7535 (t) REVERT: C 373 LYS cc_start: 0.8355 (mtpp) cc_final: 0.7902 (mtmm) REVERT: C 621 ILE cc_start: 0.8616 (mt) cc_final: 0.8407 (pt) REVERT: C 770 MET cc_start: 0.7815 (mtp) cc_final: 0.7592 (mtm) REVERT: C 966 LEU cc_start: 0.8929 (mt) cc_final: 0.8502 (mm) REVERT: C 1086 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8996 (mm) REVERT: C 1109 ASP cc_start: 0.7656 (p0) cc_final: 0.7279 (p0) outliers start: 86 outliers final: 53 residues processed: 434 average time/residue: 0.1618 time to fit residues: 112.6951 Evaluate side-chains 406 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 344 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain C residue 42 TYR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 1086 ILE Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1098 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 184 optimal weight: 5.9990 chunk 239 optimal weight: 0.1980 chunk 203 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 258 optimal weight: 0.0980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN C 939 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.133298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.103411 restraints weight = 56595.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.106182 restraints weight = 32464.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.108006 restraints weight = 22055.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.109194 restraints weight = 16941.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.109884 restraints weight = 14241.000| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 24495 Z= 0.146 Angle : 0.740 16.601 33339 Z= 0.374 Chirality : 0.047 0.230 3762 Planarity : 0.005 0.089 4302 Dihedral : 5.994 34.927 3294 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 3.25 % Allowed : 16.53 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.13 (0.15), residues: 3024 helix: 1.61 (0.21), residues: 687 sheet: -0.81 (0.21), residues: 585 loop : -3.10 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1089 TYR 0.017 0.001 TYR B 41 PHE 0.037 0.002 PHE A 231 TRP 0.028 0.001 TRP C 101 HIS 0.005 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00335 (24453) covalent geometry : angle 0.72587 (33255) SS BOND : bond 0.00382 ( 42) SS BOND : angle 2.96192 ( 84) hydrogen bonds : bond 0.03845 ( 894) hydrogen bonds : angle 5.94693 ( 2358) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 357 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.6807 (OUTLIER) cc_final: 0.5194 (t80) REVERT: A 183 ARG cc_start: 0.6274 (mmt180) cc_final: 0.5948 (mtt180) REVERT: A 216 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6729 (pp) REVERT: A 440 TYR cc_start: 0.6814 (p90) cc_final: 0.6384 (p90) REVERT: A 441 ARG cc_start: 0.6569 (mtp85) cc_final: 0.5742 (mtp85) REVERT: A 503 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7776 (mm) REVERT: A 554 ASP cc_start: 0.5923 (t0) cc_final: 0.5688 (t0) REVERT: A 558 PHE cc_start: 0.7057 (m-80) cc_final: 0.6785 (m-80) REVERT: A 837 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: A 942 ASN cc_start: 0.8609 (m-40) cc_final: 0.8352 (m-40) REVERT: A 966 LEU cc_start: 0.9118 (mm) cc_final: 0.8900 (mm) REVERT: A 1068 LYS cc_start: 0.4965 (pttm) cc_final: 0.4593 (pttp) REVERT: B 42 TYR cc_start: 0.6497 (OUTLIER) cc_final: 0.5041 (t80) REVERT: B 191 ASP cc_start: 0.7828 (t0) cc_final: 0.7251 (t0) REVERT: B 405 ILE cc_start: 0.8718 (mm) cc_final: 0.8507 (mp) REVERT: B 558 PHE cc_start: 0.7646 (m-80) cc_final: 0.7087 (m-80) REVERT: B 818 GLN cc_start: 0.7337 (mp10) cc_final: 0.7084 (mp10) REVERT: B 966 LEU cc_start: 0.9100 (mm) cc_final: 0.8790 (mm) REVERT: B 1011 MET cc_start: 0.8666 (ttm) cc_final: 0.8289 (ttm) REVERT: B 1073 ARG cc_start: 0.7941 (tmm160) cc_final: 0.7562 (tmm160) REVERT: C 42 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.4788 (t80) REVERT: C 183 ARG cc_start: 0.6126 (mmt180) cc_final: 0.5861 (mmt180) REVERT: C 285 GLU cc_start: 0.8721 (tt0) cc_final: 0.8498 (tm-30) REVERT: C 348 CYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7589 (t) REVERT: C 373 LYS cc_start: 0.8386 (mtpp) cc_final: 0.7908 (mtmm) REVERT: C 558 PHE cc_start: 0.7090 (m-80) cc_final: 0.6828 (m-80) REVERT: C 966 LEU cc_start: 0.9027 (mt) cc_final: 0.8528 (mm) outliers start: 86 outliers final: 55 residues processed: 413 average time/residue: 0.1609 time to fit residues: 107.1246 Evaluate side-chains 396 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 334 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain C residue 42 TYR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 851 MET Chi-restraints excluded: chain C residue 896 ASN Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1098 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 226 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 264 optimal weight: 0.3980 chunk 298 optimal weight: 0.5980 chunk 293 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 243 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 283 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.134131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.104205 restraints weight = 56806.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.107051 restraints weight = 32330.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.108944 restraints weight = 21819.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.110157 restraints weight = 16663.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.110911 restraints weight = 13950.531| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24495 Z= 0.131 Angle : 0.725 14.904 33339 Z= 0.367 Chirality : 0.047 0.197 3762 Planarity : 0.005 0.087 4302 Dihedral : 5.871 38.418 3294 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 2.95 % Allowed : 17.25 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.05 (0.15), residues: 3024 helix: 1.67 (0.21), residues: 687 sheet: -0.85 (0.21), residues: 570 loop : -2.99 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1089 TYR 0.025 0.001 TYR B 886 PHE 0.038 0.002 PHE C 231 TRP 0.031 0.001 TRP C 101 HIS 0.004 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00296 (24453) covalent geometry : angle 0.71279 (33255) SS BOND : bond 0.00359 ( 42) SS BOND : angle 2.75452 ( 84) hydrogen bonds : bond 0.03770 ( 894) hydrogen bonds : angle 5.84933 ( 2358) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 355 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.6789 (OUTLIER) cc_final: 0.5049 (t80) REVERT: A 183 ARG cc_start: 0.6278 (mmt180) cc_final: 0.5959 (mtt180) REVERT: A 216 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6750 (pp) REVERT: A 441 ARG cc_start: 0.6374 (mtp85) cc_final: 0.5712 (mtp85) REVERT: A 503 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7798 (mm) REVERT: A 558 PHE cc_start: 0.7117 (m-80) cc_final: 0.6785 (m-80) REVERT: A 621 ILE cc_start: 0.8769 (mt) cc_final: 0.8389 (pt) REVERT: A 837 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: A 942 ASN cc_start: 0.8620 (m-40) cc_final: 0.8371 (m-40) REVERT: A 1011 MET cc_start: 0.8739 (ttm) cc_final: 0.8408 (ttp) REVERT: A 1023 ASP cc_start: 0.7923 (m-30) cc_final: 0.7340 (m-30) REVERT: A 1068 LYS cc_start: 0.4954 (pttm) cc_final: 0.4570 (pttp) REVERT: A 1078 VAL cc_start: 0.6184 (t) cc_final: 0.5864 (t) REVERT: B 42 TYR cc_start: 0.6543 (OUTLIER) cc_final: 0.4994 (t80) REVERT: B 183 ARG cc_start: 0.6288 (mmt180) cc_final: 0.6085 (mmt180) REVERT: B 191 ASP cc_start: 0.7830 (t0) cc_final: 0.7325 (t0) REVERT: B 285 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8154 (tm-30) REVERT: B 405 ILE cc_start: 0.8721 (mm) cc_final: 0.8369 (mp) REVERT: B 440 TYR cc_start: 0.7591 (p90) cc_final: 0.6800 (p90) REVERT: B 558 PHE cc_start: 0.7646 (m-80) cc_final: 0.7070 (m-80) REVERT: B 818 GLN cc_start: 0.7284 (mp10) cc_final: 0.7048 (mp10) REVERT: B 966 LEU cc_start: 0.9145 (mm) cc_final: 0.8865 (mm) REVERT: B 1011 MET cc_start: 0.8714 (ttm) cc_final: 0.8383 (ttm) REVERT: B 1073 ARG cc_start: 0.7840 (tmm160) cc_final: 0.7543 (tmm160) REVERT: C 42 TYR cc_start: 0.6255 (OUTLIER) cc_final: 0.4600 (t80) REVERT: C 183 ARG cc_start: 0.6095 (mmt180) cc_final: 0.5791 (mmt180) REVERT: C 348 CYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7584 (t) REVERT: C 373 LYS cc_start: 0.8403 (mtpp) cc_final: 0.7908 (mtmm) REVERT: C 441 ARG cc_start: 0.6680 (mtp85) cc_final: 0.6403 (ttm-80) REVERT: C 451 PHE cc_start: 0.7233 (m-80) cc_final: 0.6881 (m-10) REVERT: C 558 PHE cc_start: 0.7085 (m-80) cc_final: 0.6736 (m-80) REVERT: C 801 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8246 (mt-10) REVERT: C 884 MET cc_start: 0.8475 (mmp) cc_final: 0.8189 (mmm) REVERT: C 966 LEU cc_start: 0.9036 (mt) cc_final: 0.8518 (mm) REVERT: C 1013 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: C 1109 ASP cc_start: 0.7739 (p0) cc_final: 0.7383 (p0) outliers start: 78 outliers final: 61 residues processed: 407 average time/residue: 0.1593 time to fit residues: 104.9722 Evaluate side-chains 408 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 339 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain C residue 42 TYR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 851 MET Chi-restraints excluded: chain C residue 896 ASN Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 1013 GLU Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1098 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 40 optimal weight: 0.9980 chunk 195 optimal weight: 0.9990 chunk 281 optimal weight: 3.9990 chunk 276 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 236 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 106 optimal weight: 0.4980 chunk 167 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN C 987 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.133871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.104130 restraints weight = 56917.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.106928 restraints weight = 32295.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.108766 restraints weight = 21786.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.109941 restraints weight = 16668.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.110747 restraints weight = 13971.564| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24495 Z= 0.136 Angle : 0.741 14.094 33339 Z= 0.374 Chirality : 0.047 0.213 3762 Planarity : 0.005 0.087 4302 Dihedral : 5.832 37.281 3294 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 3.10 % Allowed : 17.29 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.01 (0.15), residues: 3024 helix: 1.68 (0.21), residues: 687 sheet: -0.74 (0.21), residues: 567 loop : -2.99 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 38 TYR 0.026 0.001 TYR B 886 PHE 0.044 0.002 PHE C 231 TRP 0.031 0.001 TRP C 101 HIS 0.007 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00304 (24453) covalent geometry : angle 0.72816 (33255) SS BOND : bond 0.00406 ( 42) SS BOND : angle 2.82655 ( 84) hydrogen bonds : bond 0.03772 ( 894) hydrogen bonds : angle 5.81696 ( 2358) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 359 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7129 (ppp) cc_final: 0.6910 (ppp) REVERT: A 42 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.5098 (t80) REVERT: A 183 ARG cc_start: 0.6277 (mmt180) cc_final: 0.5968 (mtt180) REVERT: A 216 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6732 (pp) REVERT: A 440 TYR cc_start: 0.6693 (p90) cc_final: 0.6321 (p90) REVERT: A 441 ARG cc_start: 0.6349 (mtp85) cc_final: 0.5657 (mtp85) REVERT: A 503 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7811 (mm) REVERT: A 558 PHE cc_start: 0.7278 (m-80) cc_final: 0.6928 (m-80) REVERT: A 621 ILE cc_start: 0.8781 (mt) cc_final: 0.8409 (pt) REVERT: A 837 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: A 942 ASN cc_start: 0.8600 (m-40) cc_final: 0.8386 (m-40) REVERT: A 1011 MET cc_start: 0.8782 (ttm) cc_final: 0.8475 (ttp) REVERT: A 1023 ASP cc_start: 0.8004 (m-30) cc_final: 0.7234 (m-30) REVERT: A 1068 LYS cc_start: 0.4924 (pttm) cc_final: 0.4569 (pttp) REVERT: A 1078 VAL cc_start: 0.6183 (t) cc_final: 0.5860 (t) REVERT: B 42 TYR cc_start: 0.6576 (OUTLIER) cc_final: 0.4835 (t80) REVERT: B 191 ASP cc_start: 0.7883 (t0) cc_final: 0.7298 (t0) REVERT: B 405 ILE cc_start: 0.8715 (mm) cc_final: 0.8499 (mp) REVERT: B 558 PHE cc_start: 0.7667 (m-80) cc_final: 0.7061 (m-80) REVERT: B 723 TYR cc_start: 0.9004 (t80) cc_final: 0.8664 (t80) REVERT: B 818 GLN cc_start: 0.7489 (mp10) cc_final: 0.7187 (mp10) REVERT: B 966 LEU cc_start: 0.9177 (mm) cc_final: 0.8891 (mm) REVERT: B 1011 MET cc_start: 0.8721 (ttm) cc_final: 0.8381 (ttm) REVERT: B 1073 ARG cc_start: 0.7656 (tmm160) cc_final: 0.7352 (tmm160) REVERT: C 42 TYR cc_start: 0.6143 (OUTLIER) cc_final: 0.4435 (t80) REVERT: C 183 ARG cc_start: 0.6298 (mmt180) cc_final: 0.5953 (mmt180) REVERT: C 348 CYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7609 (t) REVERT: C 373 LYS cc_start: 0.8421 (mtpp) cc_final: 0.7918 (mtmm) REVERT: C 441 ARG cc_start: 0.6667 (mtp85) cc_final: 0.6464 (ttm-80) REVERT: C 451 PHE cc_start: 0.7229 (m-80) cc_final: 0.6820 (m-10) REVERT: C 558 PHE cc_start: 0.7064 (m-80) cc_final: 0.6693 (m-80) REVERT: C 707 GLU cc_start: 0.7757 (tt0) cc_final: 0.7519 (tt0) REVERT: C 801 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8224 (mt-10) REVERT: C 966 LEU cc_start: 0.9056 (mt) cc_final: 0.8645 (mm) REVERT: C 1013 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: C 1109 ASP cc_start: 0.7753 (p0) cc_final: 0.7405 (p0) outliers start: 82 outliers final: 66 residues processed: 416 average time/residue: 0.1570 time to fit residues: 106.0899 Evaluate side-chains 411 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 337 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain C residue 42 TYR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 896 ASN Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 1013 GLU Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1098 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 135 optimal weight: 0.0070 chunk 17 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 231 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 159 optimal weight: 0.4980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN A 984 GLN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN B 181 HIS ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.134452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.104795 restraints weight = 57185.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.107585 restraints weight = 32412.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.109477 restraints weight = 21913.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.110695 restraints weight = 16695.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.111359 restraints weight = 13965.730| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24495 Z= 0.131 Angle : 0.737 14.040 33339 Z= 0.372 Chirality : 0.047 0.189 3762 Planarity : 0.005 0.086 4302 Dihedral : 5.770 36.016 3294 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 2.88 % Allowed : 18.12 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.02 (0.15), residues: 3024 helix: 1.61 (0.21), residues: 687 sheet: -0.86 (0.21), residues: 582 loop : -2.94 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 38 TYR 0.016 0.001 TYR B 41 PHE 0.038 0.002 PHE C 231 TRP 0.035 0.001 TRP C 101 HIS 0.004 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00295 (24453) covalent geometry : angle 0.72514 (33255) SS BOND : bond 0.00371 ( 42) SS BOND : angle 2.71649 ( 84) hydrogen bonds : bond 0.03774 ( 894) hydrogen bonds : angle 5.75881 ( 2358) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 358 time to evaluate : 0.980 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 42 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.5054 (t80) REVERT: A 183 ARG cc_start: 0.6356 (mmt180) cc_final: 0.5999 (mtt180) REVERT: A 216 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6714 (pp) REVERT: A 440 TYR cc_start: 0.6662 (p90) cc_final: 0.6275 (p90) REVERT: A 441 ARG cc_start: 0.6292 (mtp85) cc_final: 0.5576 (mtp85) REVERT: A 503 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7796 (mm) REVERT: A 558 PHE cc_start: 0.7102 (m-80) cc_final: 0.6844 (m-80) REVERT: A 621 ILE cc_start: 0.8763 (mt) cc_final: 0.8424 (pt) REVERT: A 837 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: A 942 ASN cc_start: 0.8597 (m-40) cc_final: 0.8382 (m-40) REVERT: A 1023 ASP cc_start: 0.7959 (m-30) cc_final: 0.7363 (m-30) REVERT: A 1068 LYS cc_start: 0.5078 (pttm) cc_final: 0.4676 (pttp) REVERT: A 1078 VAL cc_start: 0.6228 (t) cc_final: 0.5924 (t) REVERT: B 183 ARG cc_start: 0.6499 (mmt180) cc_final: 0.6012 (mmt180) REVERT: B 191 ASP cc_start: 0.7828 (t0) cc_final: 0.7271 (t0) REVERT: B 405 ILE cc_start: 0.8737 (mm) cc_final: 0.8411 (mp) REVERT: B 440 TYR cc_start: 0.7593 (p90) cc_final: 0.6825 (p90) REVERT: B 548 PHE cc_start: 0.7695 (m-80) cc_final: 0.7432 (m-80) REVERT: B 558 PHE cc_start: 0.7644 (m-80) cc_final: 0.7098 (m-80) REVERT: B 818 GLN cc_start: 0.7494 (mp10) cc_final: 0.7130 (mp10) REVERT: B 966 LEU cc_start: 0.9174 (mm) cc_final: 0.8891 (mm) REVERT: B 1011 MET cc_start: 0.8711 (ttm) cc_final: 0.8378 (ttm) REVERT: B 1073 ARG cc_start: 0.7620 (tmm160) cc_final: 0.7316 (tmm160) REVERT: C 42 TYR cc_start: 0.6070 (OUTLIER) cc_final: 0.4342 (t80) REVERT: C 348 CYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7298 (t) REVERT: C 373 LYS cc_start: 0.8446 (mtpp) cc_final: 0.7941 (mtmm) REVERT: C 451 PHE cc_start: 0.7198 (m-80) cc_final: 0.6779 (m-10) REVERT: C 554 ASP cc_start: 0.6471 (t0) cc_final: 0.6055 (p0) REVERT: C 707 GLU cc_start: 0.7472 (tt0) cc_final: 0.7249 (tt0) REVERT: C 801 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8199 (mt-10) REVERT: C 966 LEU cc_start: 0.9032 (mt) cc_final: 0.8554 (mm) REVERT: C 967 ASP cc_start: 0.7463 (t0) cc_final: 0.7201 (m-30) REVERT: C 1013 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: C 1033 SER cc_start: 0.9339 (t) cc_final: 0.9063 (p) REVERT: C 1109 ASP cc_start: 0.7739 (p0) cc_final: 0.7395 (p0) outliers start: 76 outliers final: 61 residues processed: 409 average time/residue: 0.1560 time to fit residues: 103.6377 Evaluate side-chains 403 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 335 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 984 GLN Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain C residue 42 TYR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 1013 GLU Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1098 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 214 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 144 optimal weight: 0.0870 chunk 303 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 277 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 116 optimal weight: 0.0030 overall best weight: 1.8174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 889 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.134142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.104671 restraints weight = 56892.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.107491 restraints weight = 32268.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.109340 restraints weight = 21646.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.110539 restraints weight = 16524.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.111253 restraints weight = 13858.167| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 24495 Z= 0.202 Angle : 0.884 59.177 33339 Z= 0.471 Chirality : 0.047 0.258 3762 Planarity : 0.005 0.086 4302 Dihedral : 5.776 36.035 3294 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 2.80 % Allowed : 18.62 % Favored : 78.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.04 (0.15), residues: 3024 helix: 1.56 (0.21), residues: 687 sheet: -0.87 (0.21), residues: 582 loop : -2.94 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.026 0.001 TYR B 197 PHE 0.035 0.002 PHE C 231 TRP 0.032 0.001 TRP C 101 HIS 0.004 0.001 HIS A1065 Details of bonding type rmsd covalent geometry : bond 0.00447 (24453) covalent geometry : angle 0.85100 (33255) SS BOND : bond 0.00684 ( 42) SS BOND : angle 4.80888 ( 84) hydrogen bonds : bond 0.03832 ( 894) hydrogen bonds : angle 5.75758 ( 2358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4703.80 seconds wall clock time: 82 minutes 1.18 seconds (4921.18 seconds total)