Starting phenix.real_space_refine on Wed Aug 27 01:37:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cas_45402/08_2025/9cas_45402_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cas_45402/08_2025/9cas_45402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cas_45402/08_2025/9cas_45402_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cas_45402/08_2025/9cas_45402_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cas_45402/08_2025/9cas_45402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cas_45402/08_2025/9cas_45402.map" } resolution = 3.1 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= 0.026 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: 5 Type Number sf(0) Gaussians S 120 5.16 5 C 14542 2.51 5 N 3810 2.21 5 O 4300 1.98 5 H 22251 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45023 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 15009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 15009 Classifications: {'peptide': 975} Link IDs: {'PTRANS': 45, 'TRANS': 929} Chain breaks: 13 Chain: "B" Number of atoms: 14999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 14999 Classifications: {'peptide': 974} Link IDs: {'PTRANS': 45, 'TRANS': 928} Chain breaks: 13 Chain: "C" Number of atoms: 15015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 15015 Classifications: {'peptide': 976} Link IDs: {'PTRANS': 45, 'TRANS': 930} Chain breaks: 13 Time building chain proxies: 7.45, per 1000 atoms: 0.17 Number of scatterers: 45023 At special positions: 0 Unit cell: (115.62, 120.32, 170.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 O 4300 8.00 N 3810 7.00 C 14542 6.00 H 22251 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 160 " distance=2.06 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 349 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 420 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 512 " distance=2.03 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 636 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 658 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A1015 " - pdb=" SG CYS A1026 " distance=2.03 Simple disulfide: pdb=" SG CYS A1065 " - pdb=" SG CYS A1109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 160 " distance=2.05 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 420 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 512 " distance=2.03 Simple disulfide: pdb=" SG CYS B 468 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 604 " - pdb=" SG CYS B 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 658 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 732 " distance=2.03 Simple disulfide: pdb=" SG CYS B1015 " - pdb=" SG CYS B1026 " distance=2.03 Simple disulfide: pdb=" SG CYS B1065 " - pdb=" SG CYS B1109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 160 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 420 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 512 " distance=2.03 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 525 " - pdb=" SG CYS C 577 " distance=2.03 Simple disulfide: pdb=" SG CYS C 604 " - pdb=" SG CYS C 636 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 658 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 732 " distance=2.03 Simple disulfide: pdb=" SG CYS C1015 " - pdb=" SG CYS C1026 " distance=2.03 Simple disulfide: pdb=" SG CYS C1065 " - pdb=" SG CYS C1109 " 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: 3.37 Conformation dependent library (CDL) restraints added in 938.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5480 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 45 sheets defined 27.0% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.532A pdb=" N TRP A 341 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 359 removed outlier: 4.083A pdb=" N ASN A 358 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 377 removed outlier: 4.068A pdb=" N ASN A 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.620A pdb=" N GLN A 493 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 726 removed outlier: 3.559A pdb=" N TYR A 724 " --> pdb=" O ASP A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 738 removed outlier: 3.833A pdb=" N GLN A 738 " --> pdb=" O ASN A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 766 Processing helix chain 'A' and resid 799 through 809 Processing helix chain 'A' and resid 833 through 839 Processing helix chain 'A' and resid 849 through 868 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 880 through 891 Processing helix chain 'A' and resid 895 through 902 removed outlier: 4.346A pdb=" N LEU A 899 " --> pdb=" O THR A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 923 Processing helix chain 'A' and resid 928 through 948 removed outlier: 3.503A pdb=" N GLN A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 951 No H-bonds generated for 'chain 'A' and resid 949 through 951' Processing helix chain 'A' and resid 959 through 967 removed outlier: 3.645A pdb=" N ILE A 963 " --> pdb=" O VAL A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1016 removed outlier: 4.416A pdb=" N VAL A 974 " --> pdb=" O VAL A 970 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN A 975 " --> pdb=" O GLU A 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.516A pdb=" N TRP B 341 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 359 removed outlier: 4.159A pdb=" N ASN B 358 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 377 removed outlier: 3.974A pdb=" N ASN B 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 489 through 493 removed outlier: 3.532A pdb=" N GLN B 493 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 726 removed outlier: 3.577A pdb=" N TYR B 724 " --> pdb=" O ASP B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 738 removed outlier: 3.831A pdb=" N GLN B 738 " --> pdb=" O ASN B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 766 Processing helix chain 'B' and resid 799 through 809 removed outlier: 3.542A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 839 Processing helix chain 'B' and resid 849 through 868 Processing helix chain 'B' and resid 869 through 873 Processing helix chain 'B' and resid 880 through 891 Processing helix chain 'B' and resid 896 through 902 Processing helix chain 'B' and resid 902 through 923 Processing helix chain 'B' and resid 928 through 948 removed outlier: 3.526A pdb=" N GLN B 932 " --> pdb=" O LEU B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 951 No H-bonds generated for 'chain 'B' and resid 949 through 951' Processing helix chain 'B' and resid 959 through 967 removed outlier: 3.611A pdb=" N ILE B 963 " --> pdb=" O VAL B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 1016 removed outlier: 4.533A pdb=" N VAL B 974 " --> pdb=" O VAL B 970 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN B 975 " --> pdb=" O GLU B 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 292 Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.606A pdb=" N TRP C 341 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 359 removed outlier: 4.142A pdb=" N ASN C 358 " --> pdb=" O VAL C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 377 removed outlier: 4.034A pdb=" N ASN C 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 398 Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 489 through 493 removed outlier: 3.572A pdb=" N GLN C 493 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 726 removed outlier: 3.637A pdb=" N TYR C 724 " --> pdb=" O ASP C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 738 removed outlier: 3.836A pdb=" N GLN C 738 " --> pdb=" O ASN C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 766 Processing helix chain 'C' and resid 799 through 809 removed outlier: 3.520A pdb=" N VAL C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 839 Processing helix chain 'C' and resid 849 through 868 Processing helix chain 'C' and resid 869 through 873 Processing helix chain 'C' and resid 880 through 891 Processing helix chain 'C' and resid 895 through 902 removed outlier: 4.236A pdb=" N LEU C 899 " --> pdb=" O THR C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 923 Processing helix chain 'C' and resid 928 through 948 Processing helix chain 'C' and resid 949 through 951 No H-bonds generated for 'chain 'C' and resid 949 through 951' Processing helix chain 'C' and resid 959 through 967 removed outlier: 3.663A pdb=" N ILE C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 1016 removed outlier: 4.582A pdb=" N VAL C 974 " --> pdb=" O VAL C 970 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN C 975 " --> pdb=" O GLU C 971 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 3.609A pdb=" N VAL A 67 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ASN A 66 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N TYR A 257 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU A 195 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A 222 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 197 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR A 201 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ALA A 216 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL A 41 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 302 Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 316 Processing sheet with id=AA6, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.890A pdb=" N VAL A 383 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 349 through 350 removed outlier: 6.629A pdb=" N CYS A 349 " --> pdb=" O CYS A 512 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 440 through 442 Processing sheet with id=AA9, first strand: chain 'A' and resid 641 through 642 removed outlier: 5.738A pdb=" N GLU A 641 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N THR A 679 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 657 " --> pdb=" O ILE A 653 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 684 through 686 removed outlier: 3.788A pdb=" N SER A 686 " --> pdb=" O MET B 771 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.498A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A1033 " --> pdb=" O VAL A1048 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR A1050 " --> pdb=" O HIS A1031 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N HIS A1031 " --> pdb=" O TYR A1050 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 716 through 718 removed outlier: 4.418A pdb=" N LYS A 716 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 770 through 772 removed outlier: 5.904A pdb=" N MET A 771 " --> pdb=" O SER C 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AB6, first strand: chain 'A' and resid 1103 through 1108 removed outlier: 4.514A pdb=" N ALA A1070 " --> pdb=" O SER A1106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1077 through 1080 Processing sheet with id=AB8, first strand: chain 'B' and resid 34 through 35 removed outlier: 7.741A pdb=" N ASN B 66 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR B 257 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU B 195 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS B 222 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 197 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR B 201 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ALA B 216 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL B 41 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 54 through 60 Processing sheet with id=AC1, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AC2, first strand: chain 'B' and resid 299 through 302 Processing sheet with id=AC3, first strand: chain 'B' and resid 313 through 316 Processing sheet with id=AC4, first strand: chain 'B' and resid 344 through 346 removed outlier: 3.900A pdb=" N VAL B 383 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 349 through 350 removed outlier: 6.637A pdb=" N CYS B 349 " --> pdb=" O CYS B 512 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 440 through 442 Processing sheet with id=AC7, first strand: chain 'B' and resid 641 through 642 removed outlier: 5.769A pdb=" N GLU B 641 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N THR B 679 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ALA B 659 " --> pdb=" O PRO B 652 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 684 through 686 removed outlier: 7.109A pdb=" N ALA B 684 " --> pdb=" O MET C 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 694 through 711 removed outlier: 6.514A pdb=" N THR B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR B1059 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLU B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET B1033 " --> pdb=" O VAL B1048 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR B1050 " --> pdb=" O HIS B1031 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N HIS B1031 " --> pdb=" O TYR B1050 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 716 through 718 removed outlier: 4.506A pdb=" N LYS B 716 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AD3, first strand: chain 'B' and resid 1103 through 1108 removed outlier: 4.308A pdb=" N ALA B1070 " --> pdb=" O SER B1106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1077 through 1080 Processing sheet with id=AD5, first strand: chain 'C' and resid 34 through 35 removed outlier: 3.544A pdb=" N VAL C 67 " --> pdb=" O PHE C 34 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN C 66 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR C 257 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU C 195 " --> pdb=" O LYS C 222 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS C 222 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 197 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TYR C 201 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ALA C 216 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL C 41 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 54 through 60 Processing sheet with id=AD7, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.614A pdb=" N GLY C 101 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 299 through 302 Processing sheet with id=AD9, first strand: chain 'C' and resid 313 through 316 Processing sheet with id=AE1, first strand: chain 'C' and resid 342 through 346 removed outlier: 3.602A pdb=" N GLU C 342 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 387 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL C 383 " --> pdb=" O ILE C 346 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 349 through 350 removed outlier: 6.585A pdb=" N CYS C 349 " --> pdb=" O CYS C 512 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 440 through 442 Processing sheet with id=AE4, first strand: chain 'C' and resid 641 through 642 removed outlier: 5.656A pdb=" N GLU C 641 " --> pdb=" O ALA C 677 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N THR C 679 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ALA C 659 " --> pdb=" O PRO C 652 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.505A pdb=" N THR C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR C1059 " --> pdb=" O THR C 694 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C1033 " --> pdb=" O VAL C1048 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N TYR C1050 " --> pdb=" O HIS C1031 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS C1031 " --> pdb=" O TYR C1050 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 716 through 718 removed outlier: 4.386A pdb=" N LYS C 716 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 779 through 780 Processing sheet with id=AE8, first strand: chain 'C' and resid 1103 through 1108 removed outlier: 4.480A pdb=" N ALA C1070 " --> pdb=" O SER C1106 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1077 through 1080 981 hydrogen bonds defined for protein. 2562 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: 10.81 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 22251 1.04 - 1.23: 1178 1.23 - 1.43: 8779 1.43 - 1.63: 13145 1.63 - 1.83: 159 Bond restraints: 45512 Sorted by residual: bond pdb=" N THR B 922 " pdb=" CA THR B 922 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.30e-02 5.92e+03 1.09e+01 bond pdb=" N THR A 922 " pdb=" CA THR A 922 " ideal model delta sigma weight residual 1.459 1.499 -0.041 1.28e-02 6.10e+03 1.00e+01 bond pdb=" N THR C 922 " pdb=" CA THR C 922 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.23e-02 6.61e+03 8.50e+00 bond pdb=" N THR A 926 " pdb=" CA THR A 926 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.76e+00 bond pdb=" N THR A 923 " pdb=" H THR A 923 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.67e+00 ... (remaining 45507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 78600 1.25 - 2.50: 2929 2.50 - 3.74: 281 3.74 - 4.99: 59 4.99 - 6.24: 4 Bond angle restraints: 81873 Sorted by residual: angle pdb=" C THR C 922 " pdb=" N THR C 923 " pdb=" CA THR C 923 " ideal model delta sigma weight residual 120.95 126.47 -5.52 1.40e+00 5.10e-01 1.55e+01 angle pdb=" N GLY C 87 " pdb=" CA GLY C 87 " pdb=" C GLY C 87 " ideal model delta sigma weight residual 111.95 108.25 3.70 9.50e-01 1.11e+00 1.52e+01 angle pdb=" N GLY A 87 " pdb=" CA GLY A 87 " pdb=" C GLY A 87 " ideal model delta sigma weight residual 111.95 108.36 3.59 9.50e-01 1.11e+00 1.43e+01 angle pdb=" CA SER B 925 " pdb=" C SER B 925 " pdb=" O SER B 925 " ideal model delta sigma weight residual 121.45 117.43 4.02 1.07e+00 8.73e-01 1.41e+01 angle pdb=" CA SER C 925 " pdb=" C SER C 925 " pdb=" O SER C 925 " ideal model delta sigma weight residual 121.40 117.26 4.14 1.11e+00 8.12e-01 1.39e+01 ... (remaining 81868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 19370 17.94 - 35.88: 1791 35.88 - 53.82: 535 53.82 - 71.76: 110 71.76 - 89.69: 57 Dihedral angle restraints: 21863 sinusoidal: 11662 harmonic: 10201 Sorted by residual: dihedral pdb=" CB CYS A 129 " pdb=" SG CYS A 129 " pdb=" SG CYS A 160 " pdb=" CB CYS A 160 " ideal model delta sinusoidal sigma weight residual 93.00 30.62 62.38 1 1.00e+01 1.00e-02 5.15e+01 dihedral pdb=" CB CYS C 129 " pdb=" SG CYS C 129 " pdb=" SG CYS C 160 " pdb=" CB CYS C 160 " ideal model delta sinusoidal sigma weight residual 93.00 38.90 54.10 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CA TYR B 599 " pdb=" C TYR B 599 " pdb=" N GLN B 600 " pdb=" CA GLN B 600 " ideal model delta harmonic sigma weight residual -180.00 -158.18 -21.82 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 21860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2327 0.035 - 0.069: 873 0.069 - 0.104: 268 0.104 - 0.139: 135 0.139 - 0.174: 10 Chirality restraints: 3613 Sorted by residual: chirality pdb=" CA ILE C 117 " pdb=" N ILE C 117 " pdb=" C ILE C 117 " pdb=" CB ILE C 117 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA ILE A 117 " pdb=" N ILE A 117 " pdb=" C ILE A 117 " pdb=" CB ILE A 117 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CA LEU A 921 " pdb=" N LEU A 921 " pdb=" C LEU A 921 " pdb=" CB LEU A 921 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.09e-01 ... (remaining 3610 not shown) Planarity restraints: 6822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 159 " -0.251 2.00e-02 2.50e+03 3.31e-01 1.64e+03 pdb=" CG ASN B 159 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN B 159 " 0.248 2.00e-02 2.50e+03 pdb=" ND2 ASN B 159 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 159 " 0.509 2.00e-02 2.50e+03 pdb="HD22 ASN B 159 " -0.521 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 159 " -0.083 2.00e-02 2.50e+03 8.87e-02 1.18e+02 pdb=" CG ASN A 159 " 0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN A 159 " 0.081 2.00e-02 2.50e+03 pdb=" ND2 ASN A 159 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 159 " 0.129 2.00e-02 2.50e+03 pdb="HD22 ASN A 159 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 160 " 0.015 2.00e-02 2.50e+03 2.67e-02 7.15e+00 pdb=" N THR B 161 " -0.046 2.00e-02 2.50e+03 pdb=" CA THR B 161 " 0.012 2.00e-02 2.50e+03 pdb=" H THR B 161 " 0.019 2.00e-02 2.50e+03 ... (remaining 6819 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1594 2.15 - 2.76: 83770 2.76 - 3.38: 122227 3.38 - 3.99: 161721 3.99 - 4.60: 252429 Nonbonded interactions: 621741 Sorted by model distance: nonbonded pdb=" HG1 THR A 699 " pdb=" O GLN A1054 " model vdw 1.540 2.450 nonbonded pdb=" O ASN A 722 " pdb=" H GLY A 727 " model vdw 1.553 2.450 nonbonded pdb=" HG1 THR B 699 " pdb=" O GLN B1054 " model vdw 1.556 2.450 nonbonded pdb=" O ASN C 722 " pdb=" H GLY C 727 " model vdw 1.556 2.450 nonbonded pdb=" HG1 THR C 699 " pdb=" O GLN C1054 " model vdw 1.560 2.450 ... (remaining 621736 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 204 or resid 214 through 737 or (resid 738 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3)) or resid 739 through 1027 or (resid 1028 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 o \ r name HE2 or name HE3)) or resid 1029 through 1030 or (resid 1031 and (name N o \ r name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or n \ ame CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or \ name HE1 or name HE2)) or resid 1032 through 1124)) selection = (chain 'B' and (resid 33 through 737 or (resid 738 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3)) or resid 739 throu \ gh 1027 or (resid 1028 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name CE or name NZ or name H or name HA or name HB2 or nam \ e HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3)) \ or resid 1029 through 1124)) selection = (chain 'C' and (resid 33 through 165 or resid 183 through 204 or resid 214 throu \ gh 1030 or (resid 1031 and (name N or name CA or name C or name O or name CB or \ name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or \ name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 1032 through \ 1124)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.150 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: 0.310 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 37.640 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23300 Z= 0.188 Angle : 0.576 6.240 31677 Z= 0.339 Chirality : 0.044 0.174 3613 Planarity : 0.003 0.028 4074 Dihedral : 15.285 89.694 8269 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.47 % Allowed : 15.24 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.15), residues: 2841 helix: 1.99 (0.21), residues: 650 sheet: 0.04 (0.21), residues: 599 loop : -0.89 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1022 TYR 0.015 0.001 TYR A 623 PHE 0.014 0.001 PHE B 579 TRP 0.007 0.001 TRP A 341 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00364 (23261) covalent geometry : angle 0.57417 (31599) SS BOND : bond 0.00541 ( 39) SS BOND : angle 1.13979 ( 78) hydrogen bonds : bond 0.12871 ( 981) hydrogen bonds : angle 6.80205 ( 2562) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 922 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8172 (t) REVERT: B 773 LYS cc_start: 0.8548 (tppt) cc_final: 0.8250 (mmtm) outliers start: 12 outliers final: 2 residues processed: 222 average time/residue: 0.2940 time to fit residues: 108.3379 Evaluate side-chains 202 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 199 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 922 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.3980 chunk 111 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN C 600 GLN C 628 ASN C 896 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.129434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112097 restraints weight = 82632.215| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.16 r_work: 0.3203 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.0642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23300 Z= 0.169 Angle : 0.507 4.996 31677 Z= 0.271 Chirality : 0.044 0.178 3613 Planarity : 0.004 0.070 4074 Dihedral : 4.211 50.495 3125 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 1.34 % Allowed : 13.98 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.15), residues: 2841 helix: 1.98 (0.20), residues: 634 sheet: -0.01 (0.21), residues: 605 loop : -0.95 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 496 TYR 0.019 0.001 TYR A 623 PHE 0.025 0.001 PHE B 579 TRP 0.007 0.001 TRP C 869 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00402 (23261) covalent geometry : angle 0.50408 (31599) SS BOND : bond 0.00242 ( 39) SS BOND : angle 1.15353 ( 78) hydrogen bonds : bond 0.04146 ( 981) hydrogen bonds : angle 5.38980 ( 2562) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 533 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.5835 (mm) REVERT: B 777 LEU cc_start: 0.7622 (tp) cc_final: 0.7360 (tt) REVERT: C 1110 ASP cc_start: 0.7865 (t0) cc_final: 0.7659 (t0) outliers start: 34 outliers final: 29 residues processed: 235 average time/residue: 0.2850 time to fit residues: 112.9497 Evaluate side-chains 220 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 367 CYS Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 896 GLN Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 6 optimal weight: 1.9990 chunk 289 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 271 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 193 optimal weight: 0.3980 chunk 278 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 627 ASN B1037 GLN C 600 GLN C 628 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112344 restraints weight = 82556.036| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.15 r_work: 0.3204 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23300 Z= 0.137 Angle : 0.479 8.444 31677 Z= 0.254 Chirality : 0.043 0.174 3613 Planarity : 0.003 0.046 4074 Dihedral : 4.001 25.116 3120 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.26 % Allowed : 13.94 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.15), residues: 2841 helix: 1.99 (0.20), residues: 640 sheet: 0.09 (0.21), residues: 587 loop : -0.94 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 454 TYR 0.014 0.001 TYR A 623 PHE 0.017 0.001 PHE B 579 TRP 0.007 0.001 TRP A 424 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00327 (23261) covalent geometry : angle 0.47721 (31599) SS BOND : bond 0.00402 ( 39) SS BOND : angle 1.00875 ( 78) hydrogen bonds : bond 0.04004 ( 981) hydrogen bonds : angle 5.21057 ( 2562) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 579 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.5216 (p90) REVERT: B 1075 GLU cc_start: 0.7032 (pm20) cc_final: 0.6712 (pm20) outliers start: 32 outliers final: 25 residues processed: 215 average time/residue: 0.2789 time to fit residues: 100.8318 Evaluate side-chains 211 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 579 PHE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 191 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 280 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN C 600 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111539 restraints weight = 82912.422| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.15 r_work: 0.3197 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 23300 Z= 0.147 Angle : 0.478 7.592 31677 Z= 0.253 Chirality : 0.043 0.176 3613 Planarity : 0.003 0.048 4074 Dihedral : 3.988 27.355 3120 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.73 % Allowed : 13.90 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.15), residues: 2841 helix: 1.97 (0.20), residues: 642 sheet: 0.07 (0.21), residues: 610 loop : -0.95 (0.14), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 442 TYR 0.019 0.001 TYR A 623 PHE 0.019 0.001 PHE B 579 TRP 0.007 0.001 TRP A 424 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00355 (23261) covalent geometry : angle 0.47527 (31599) SS BOND : bond 0.00303 ( 39) SS BOND : angle 1.13179 ( 78) hydrogen bonds : bond 0.03916 ( 981) hydrogen bonds : angle 5.01269 ( 2562) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 769 LYS cc_start: 0.8532 (mmtp) cc_final: 0.7930 (mtmm) REVERT: B 579 PHE cc_start: 0.6136 (OUTLIER) cc_final: 0.5137 (p90) REVERT: B 777 LEU cc_start: 0.7624 (tp) cc_final: 0.7371 (tt) REVERT: B 1075 GLU cc_start: 0.7081 (pm20) cc_final: 0.6707 (pm20) REVERT: C 887 TYR cc_start: 0.8451 (t80) cc_final: 0.7992 (t80) outliers start: 44 outliers final: 29 residues processed: 233 average time/residue: 0.2756 time to fit residues: 106.8056 Evaluate side-chains 218 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 579 PHE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1050 TYR Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 215 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 236 optimal weight: 2.9990 chunk 247 optimal weight: 0.7980 chunk 238 optimal weight: 2.9990 chunk 249 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 237 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN B 916 GLN C 600 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.111751 restraints weight = 82676.048| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.14 r_work: 0.3199 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23300 Z= 0.138 Angle : 0.479 7.034 31677 Z= 0.254 Chirality : 0.043 0.174 3613 Planarity : 0.003 0.036 4074 Dihedral : 3.936 25.956 3120 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.54 % Allowed : 14.06 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.15), residues: 2841 helix: 1.95 (0.20), residues: 648 sheet: 0.14 (0.21), residues: 603 loop : -0.93 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 454 TYR 0.017 0.001 TYR A1050 PHE 0.015 0.001 PHE B 579 TRP 0.007 0.001 TRP A 424 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00332 (23261) covalent geometry : angle 0.47375 (31599) SS BOND : bond 0.00332 ( 39) SS BOND : angle 1.52245 ( 78) hydrogen bonds : bond 0.03817 ( 981) hydrogen bonds : angle 4.96513 ( 2562) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8182 (mt) REVERT: A 769 LYS cc_start: 0.8537 (mmtp) cc_final: 0.7930 (mtmm) REVERT: A 971 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7651 (mt-10) REVERT: B 579 PHE cc_start: 0.6223 (OUTLIER) cc_final: 0.5177 (p90) REVERT: B 1075 GLU cc_start: 0.7085 (pm20) cc_final: 0.6678 (pm20) REVERT: C 714 MET cc_start: 0.8864 (ptm) cc_final: 0.8474 (ptt) REVERT: C 887 TYR cc_start: 0.8410 (t80) cc_final: 0.8026 (t80) outliers start: 39 outliers final: 28 residues processed: 222 average time/residue: 0.2972 time to fit residues: 109.6452 Evaluate side-chains 215 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 579 PHE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1050 TYR Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 0.6980 chunk 249 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 172 optimal weight: 0.3980 chunk 204 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN C 600 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110655 restraints weight = 83756.618| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.15 r_work: 0.3140 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 23300 Z= 0.164 Angle : 0.496 6.932 31677 Z= 0.263 Chirality : 0.044 0.177 3613 Planarity : 0.003 0.040 4074 Dihedral : 3.976 31.538 3120 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.73 % Allowed : 13.90 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.08 (0.15), residues: 2841 helix: 1.87 (0.20), residues: 652 sheet: 0.10 (0.21), residues: 606 loop : -0.97 (0.14), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1056 TYR 0.019 0.001 TYR A 623 PHE 0.019 0.001 PHE B 579 TRP 0.007 0.001 TRP C 869 HIS 0.005 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00404 (23261) covalent geometry : angle 0.48687 (31599) SS BOND : bond 0.00389 ( 39) SS BOND : angle 2.00276 ( 78) hydrogen bonds : bond 0.03959 ( 981) hydrogen bonds : angle 4.94912 ( 2562) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8192 (mt) REVERT: A 769 LYS cc_start: 0.8546 (mmtp) cc_final: 0.7964 (mtmm) REVERT: A 811 LEU cc_start: 0.8123 (tp) cc_final: 0.7788 (tp) REVERT: A 971 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7683 (mt-10) REVERT: A 1116 ILE cc_start: 0.7320 (OUTLIER) cc_final: 0.6986 (tt) REVERT: B 579 PHE cc_start: 0.6207 (OUTLIER) cc_final: 0.5104 (p90) REVERT: B 769 LYS cc_start: 0.8691 (mmtp) cc_final: 0.8007 (mtmm) REVERT: B 777 LEU cc_start: 0.7608 (tp) cc_final: 0.7353 (tt) REVERT: B 1075 GLU cc_start: 0.7193 (pm20) cc_final: 0.6770 (pm20) REVERT: C 645 THR cc_start: 0.8510 (m) cc_final: 0.8228 (p) REVERT: C 887 TYR cc_start: 0.8452 (t80) cc_final: 0.8072 (t80) outliers start: 44 outliers final: 33 residues processed: 233 average time/residue: 0.2687 time to fit residues: 106.2633 Evaluate side-chains 231 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 579 PHE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 1050 TYR Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 259 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 210 optimal weight: 0.5980 chunk 265 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 chunk 206 optimal weight: 0.6980 chunk 283 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.126957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109698 restraints weight = 83903.207| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.15 r_work: 0.3171 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 23300 Z= 0.130 Angle : 0.479 7.834 31677 Z= 0.254 Chirality : 0.043 0.181 3613 Planarity : 0.003 0.033 4074 Dihedral : 3.902 30.980 3120 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.54 % Allowed : 14.42 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: 0.04 (0.15), residues: 2841 helix: 1.96 (0.20), residues: 654 sheet: 0.14 (0.21), residues: 604 loop : -0.87 (0.14), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1022 TYR 0.014 0.001 TYR A1050 PHE 0.015 0.001 PHE B 579 TRP 0.007 0.001 TRP A 424 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00317 (23261) covalent geometry : angle 0.47250 (31599) SS BOND : bond 0.00381 ( 39) SS BOND : angle 1.65881 ( 78) hydrogen bonds : bond 0.03806 ( 981) hydrogen bonds : angle 4.91796 ( 2562) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8215 (mt) REVERT: A 769 LYS cc_start: 0.8536 (mmtp) cc_final: 0.7960 (mtmm) REVERT: A 811 LEU cc_start: 0.8106 (tp) cc_final: 0.7770 (tp) REVERT: A 971 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7701 (mt-10) REVERT: B 579 PHE cc_start: 0.6292 (OUTLIER) cc_final: 0.5242 (p90) REVERT: B 769 LYS cc_start: 0.8693 (mmtp) cc_final: 0.8001 (mtmm) REVERT: B 918 GLN cc_start: 0.7405 (tt0) cc_final: 0.7144 (tt0) REVERT: B 1075 GLU cc_start: 0.7129 (pm20) cc_final: 0.6714 (pm20) REVERT: C 645 THR cc_start: 0.8500 (m) cc_final: 0.8218 (p) REVERT: C 714 MET cc_start: 0.8891 (ptm) cc_final: 0.8507 (ptt) REVERT: C 887 TYR cc_start: 0.8464 (t80) cc_final: 0.8093 (t80) outliers start: 39 outliers final: 34 residues processed: 232 average time/residue: 0.2724 time to fit residues: 107.1819 Evaluate side-chains 229 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 579 PHE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 1050 TYR Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 600 GLN Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 14 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 235 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 224 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 287 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.128548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111347 restraints weight = 83597.165| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.14 r_work: 0.3171 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23300 Z= 0.138 Angle : 0.481 9.803 31677 Z= 0.255 Chirality : 0.043 0.189 3613 Planarity : 0.003 0.036 4074 Dihedral : 3.887 32.507 3120 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.58 % Allowed : 14.57 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: 0.02 (0.15), residues: 2841 helix: 1.97 (0.20), residues: 652 sheet: 0.15 (0.21), residues: 599 loop : -0.89 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 442 TYR 0.013 0.001 TYR A1050 PHE 0.017 0.001 PHE B 579 TRP 0.007 0.001 TRP A 424 HIS 0.004 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00334 (23261) covalent geometry : angle 0.47298 (31599) SS BOND : bond 0.00288 ( 39) SS BOND : angle 1.85227 ( 78) hydrogen bonds : bond 0.03826 ( 981) hydrogen bonds : angle 4.89261 ( 2562) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Evaluate side-chains 234 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8229 (mt) REVERT: A 769 LYS cc_start: 0.8580 (mmtp) cc_final: 0.7987 (mtmm) REVERT: A 811 LEU cc_start: 0.8134 (tp) cc_final: 0.7789 (tp) REVERT: A 971 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7736 (mt-10) REVERT: B 579 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.5128 (p90) REVERT: B 769 LYS cc_start: 0.8695 (mmtp) cc_final: 0.8002 (mtmm) REVERT: B 918 GLN cc_start: 0.7400 (tt0) cc_final: 0.7139 (tt0) REVERT: B 1075 GLU cc_start: 0.7176 (pm20) cc_final: 0.6768 (pm20) REVERT: C 645 THR cc_start: 0.8497 (m) cc_final: 0.8216 (p) REVERT: C 714 MET cc_start: 0.8884 (ptm) cc_final: 0.8502 (ptt) REVERT: C 887 TYR cc_start: 0.8465 (t80) cc_final: 0.8093 (t80) outliers start: 40 outliers final: 37 residues processed: 227 average time/residue: 0.2638 time to fit residues: 101.0808 Evaluate side-chains 232 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 579 PHE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 1050 TYR Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 251 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107655 restraints weight = 85054.744| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.14 r_work: 0.3143 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 23300 Z= 0.186 Angle : 0.513 8.512 31677 Z= 0.273 Chirality : 0.044 0.182 3613 Planarity : 0.004 0.035 4074 Dihedral : 4.077 32.760 3120 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.81 % Allowed : 14.38 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.16 (0.15), residues: 2841 helix: 1.77 (0.20), residues: 658 sheet: 0.10 (0.21), residues: 596 loop : -1.02 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 233 TYR 0.021 0.001 TYR A 623 PHE 0.015 0.001 PHE A 84 TRP 0.008 0.001 TRP C 869 HIS 0.006 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00453 (23261) covalent geometry : angle 0.50608 (31599) SS BOND : bond 0.00332 ( 39) SS BOND : angle 1.79745 ( 78) hydrogen bonds : bond 0.04235 ( 981) hydrogen bonds : angle 4.95739 ( 2562) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.6809 (ttp-170) cc_final: 0.6466 (ttp-170) REVERT: A 422 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8240 (mt) REVERT: A 697 ILE cc_start: 0.8339 (pt) cc_final: 0.8065 (mt) REVERT: A 769 LYS cc_start: 0.8604 (mmtp) cc_final: 0.7996 (mtmm) REVERT: A 811 LEU cc_start: 0.8144 (tp) cc_final: 0.7829 (tp) REVERT: A 971 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7780 (mt-10) REVERT: A 1110 ASP cc_start: 0.7791 (t0) cc_final: 0.7577 (t0) REVERT: B 579 PHE cc_start: 0.6256 (OUTLIER) cc_final: 0.5276 (p90) REVERT: B 769 LYS cc_start: 0.8673 (mmtp) cc_final: 0.7982 (mtmm) REVERT: B 1075 GLU cc_start: 0.7206 (pm20) cc_final: 0.6773 (pm20) REVERT: C 645 THR cc_start: 0.8483 (m) cc_final: 0.8188 (p) REVERT: C 887 TYR cc_start: 0.8504 (t80) cc_final: 0.7959 (t80) outliers start: 46 outliers final: 42 residues processed: 236 average time/residue: 0.2585 time to fit residues: 101.5808 Evaluate side-chains 241 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 579 PHE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 1050 TYR Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1067 GLU Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 247 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 190 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.126465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109266 restraints weight = 84758.573| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.14 r_work: 0.3165 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23300 Z= 0.129 Angle : 0.471 6.364 31677 Z= 0.249 Chirality : 0.043 0.171 3613 Planarity : 0.003 0.036 4074 Dihedral : 3.940 32.665 3120 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.50 % Allowed : 14.85 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.02 (0.15), residues: 2841 helix: 1.96 (0.20), residues: 652 sheet: 0.09 (0.21), residues: 604 loop : -0.92 (0.14), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1022 TYR 0.013 0.001 TYR A1050 PHE 0.017 0.001 PHE B 579 TRP 0.007 0.001 TRP A 424 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00313 (23261) covalent geometry : angle 0.46626 (31599) SS BOND : bond 0.00322 ( 39) SS BOND : angle 1.47049 ( 78) hydrogen bonds : bond 0.03825 ( 981) hydrogen bonds : angle 4.89991 ( 2562) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue LYS 1028 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.6781 (ttp-170) cc_final: 0.6435 (ttp-170) REVERT: A 422 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8238 (mt) REVERT: A 697 ILE cc_start: 0.8327 (pt) cc_final: 0.8038 (mt) REVERT: A 769 LYS cc_start: 0.8607 (mmtp) cc_final: 0.8005 (mtmm) REVERT: A 811 LEU cc_start: 0.8088 (tp) cc_final: 0.7809 (tp) REVERT: A 971 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7757 (mt-10) REVERT: A 1110 ASP cc_start: 0.7830 (t0) cc_final: 0.7619 (t0) REVERT: B 579 PHE cc_start: 0.6374 (OUTLIER) cc_final: 0.5383 (p90) REVERT: B 769 LYS cc_start: 0.8688 (mmtp) cc_final: 0.7997 (mtmm) REVERT: B 1075 GLU cc_start: 0.7194 (pm20) cc_final: 0.6775 (pm20) REVERT: C 645 THR cc_start: 0.8465 (m) cc_final: 0.8167 (p) REVERT: C 887 TYR cc_start: 0.8478 (t80) cc_final: 0.8103 (t80) outliers start: 38 outliers final: 36 residues processed: 230 average time/residue: 0.2929 time to fit residues: 112.9850 Evaluate side-chains 235 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 579 PHE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 1050 TYR Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 1064 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 155 optimal weight: 0.0770 chunk 90 optimal weight: 0.9990 chunk 111 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 269 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109498 restraints weight = 84278.117| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.15 r_work: 0.3167 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23300 Z= 0.124 Angle : 0.466 5.989 31677 Z= 0.246 Chirality : 0.043 0.170 3613 Planarity : 0.003 0.033 4074 Dihedral : 3.871 31.698 3120 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.58 % Allowed : 14.97 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: 0.04 (0.15), residues: 2841 helix: 2.02 (0.20), residues: 652 sheet: 0.16 (0.21), residues: 599 loop : -0.90 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 442 TYR 0.014 0.001 TYR A1050 PHE 0.015 0.001 PHE B 579 TRP 0.007 0.001 TRP A 424 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00300 (23261) covalent geometry : angle 0.46091 (31599) SS BOND : bond 0.00297 ( 39) SS BOND : angle 1.45470 ( 78) hydrogen bonds : bond 0.03723 ( 981) hydrogen bonds : angle 4.83602 ( 2562) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8664.96 seconds wall clock time: 147 minutes 36.56 seconds (8856.56 seconds total)