Starting phenix.real_space_refine on Thu Dec 26 11:57:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cas_45402/12_2024/9cas_45402_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cas_45402/12_2024/9cas_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cas_45402/12_2024/9cas_45402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cas_45402/12_2024/9cas_45402.map" model { file = "/net/cci-nas-00/data/ceres_data/9cas_45402/12_2024/9cas_45402_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cas_45402/12_2024/9cas_45402_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 2.99s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 23.70, per 1000 atoms: 0.53 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: 11.12 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 5.50 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: 23.33 Time building geometry restraints manager: 13.40 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: 13.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.910 Extract box with map and model: 1.670 Check model and map are aligned: 0.300 Set scattering table: 0.390 Process input model: 101.080 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.150 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.970 ------------------------------------------------------------------------------- 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 23261 Z= 0.233 Angle : 0.574 6.240 31599 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 : 5.84 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP A 341 HIS 0.004 0.001 HIS B 54 PHE 0.014 0.001 PHE B 579 TYR 0.015 0.001 TYR A 623 ARG 0.004 0.000 ARG C1022 *********************** 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 : 3.266 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: 0.7023 time to fit residues: 256.8003 Evaluate side-chains 201 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 198 time to evaluate : 3.956 ------------------------------------------------------------------------------- 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 245 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 228 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN C 628 ASN C 896 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.0562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23261 Z= 0.224 Angle : 0.490 4.901 31599 Z= 0.261 Chirality : 0.043 0.175 3613 Planarity : 0.004 0.063 4074 Dihedral : 4.142 51.151 3125 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 1.14 % Allowed : 13.82 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 2841 helix: 1.95 (0.20), residues: 646 sheet: 0.02 (0.21), residues: 604 loop : -0.93 (0.14), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 424 HIS 0.006 0.001 HIS B 54 PHE 0.024 0.001 PHE B 579 TYR 0.017 0.001 TYR A 623 ARG 0.004 0.000 ARG C1022 *********************** 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 232 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 23 residues processed: 227 average time/residue: 0.6929 time to fit residues: 261.6246 Evaluate side-chains 207 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 335 PHE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 776 THR 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 367 CYS 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 146 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 219 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 chunk 285 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 23261 Z= 0.324 Angle : 0.518 9.481 31599 Z= 0.277 Chirality : 0.045 0.183 3613 Planarity : 0.004 0.050 4074 Dihedral : 4.151 23.106 3120 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.21 % Rotamer: Outliers : 1.58 % Allowed : 14.30 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 2841 helix: 1.88 (0.20), residues: 635 sheet: -0.05 (0.20), residues: 618 loop : -1.03 (0.14), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 869 HIS 0.006 0.001 HIS B 54 PHE 0.017 0.001 PHE B 579 TYR 0.023 0.001 TYR A 623 ARG 0.004 0.000 ARG C 454 *********************** 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 239 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 3.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 769 LYS cc_start: 0.8456 (mmtp) cc_final: 0.7910 (mtmm) REVERT: B 533 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.5860 (mm) REVERT: B 579 PHE cc_start: 0.6136 (OUTLIER) cc_final: 0.5233 (p90) REVERT: B 777 LEU cc_start: 0.7692 (tp) cc_final: 0.7429 (tt) REVERT: B 1075 GLU cc_start: 0.7065 (pm20) cc_final: 0.6728 (pm20) outliers start: 40 outliers final: 31 residues processed: 231 average time/residue: 0.6822 time to fit residues: 264.2404 Evaluate side-chains 229 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 3.682 ------------------------------------------------------------------------------- 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 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 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 533 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 50 SER 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 624 SER 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 261 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 126 optimal weight: 0.2980 chunk 177 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 251 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 GLN B1037 GLN C 600 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 23261 Z= 0.195 Angle : 0.474 7.077 31599 Z= 0.251 Chirality : 0.043 0.174 3613 Planarity : 0.003 0.043 4074 Dihedral : 3.996 27.454 3120 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.54 % Allowed : 14.30 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 2841 helix: 1.94 (0.20), residues: 642 sheet: 0.09 (0.21), residues: 597 loop : -0.95 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 869 HIS 0.005 0.001 HIS B 54 PHE 0.020 0.001 PHE B 579 TYR 0.017 0.001 TYR A1050 ARG 0.002 0.000 ARG C1022 *********************** 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 233 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 3.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 769 LYS cc_start: 0.8455 (mmtp) cc_final: 0.7906 (mtmm) REVERT: B 579 PHE cc_start: 0.6071 (OUTLIER) cc_final: 0.5113 (p90) REVERT: B 777 LEU cc_start: 0.7674 (tp) cc_final: 0.7418 (tt) REVERT: B 1075 GLU cc_start: 0.7085 (pm20) cc_final: 0.6688 (pm20) outliers start: 39 outliers final: 29 residues processed: 226 average time/residue: 0.7578 time to fit residues: 284.2312 Evaluate side-chains 216 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 3.595 ------------------------------------------------------------------------------- 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 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 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 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 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 1064 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 0.4980 chunk 159 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 143 optimal weight: 0.4980 chunk 252 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 23261 Z= 0.298 Angle : 0.501 7.816 31599 Z= 0.267 Chirality : 0.044 0.179 3613 Planarity : 0.004 0.045 4074 Dihedral : 4.078 25.888 3120 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.89 % Allowed : 13.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 2841 helix: 1.86 (0.20), residues: 642 sheet: 0.08 (0.21), residues: 598 loop : -1.03 (0.14), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 424 HIS 0.006 0.001 HIS B 54 PHE 0.017 0.001 PHE B 579 TYR 0.020 0.001 TYR A 623 ARG 0.003 0.000 ARG C 454 *********************** 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 246 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 3.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8411 (mt) REVERT: A 769 LYS cc_start: 0.8490 (mmtp) cc_final: 0.7921 (mtmm) REVERT: A 971 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7634 (mt-10) REVERT: B 533 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.5931 (mm) REVERT: B 579 PHE cc_start: 0.6183 (OUTLIER) cc_final: 0.5298 (p90) REVERT: B 777 LEU cc_start: 0.7693 (tp) cc_final: 0.7434 (tt) REVERT: B 918 GLN cc_start: 0.7527 (tt0) cc_final: 0.7294 (tt0) REVERT: B 1056 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7993 (ttt180) REVERT: B 1075 GLU cc_start: 0.7161 (pm20) cc_final: 0.6755 (pm20) REVERT: C 645 THR cc_start: 0.8590 (m) cc_final: 0.8314 (p) REVERT: C 887 TYR cc_start: 0.8351 (t80) cc_final: 0.7866 (t80) outliers start: 48 outliers final: 33 residues processed: 237 average time/residue: 0.7013 time to fit residues: 277.0011 Evaluate side-chains 230 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 3.381 ------------------------------------------------------------------------------- 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 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 422 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 579 PHE Chi-restraints excluded: chain B residue 583 SER 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 1056 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 1.9990 chunk 253 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 281 optimal weight: 0.7980 chunk 233 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN B 628 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 23261 Z= 0.228 Angle : 0.481 7.271 31599 Z= 0.255 Chirality : 0.043 0.175 3613 Planarity : 0.003 0.034 4074 Dihedral : 4.003 29.226 3120 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.69 % Allowed : 14.22 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 2841 helix: 1.82 (0.20), residues: 660 sheet: 0.10 (0.21), residues: 603 loop : -0.95 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 869 HIS 0.004 0.001 HIS B 54 PHE 0.018 0.001 PHE B 579 TYR 0.015 0.001 TYR A 623 ARG 0.002 0.000 ARG B 442 *********************** 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 237 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8417 (mt) REVERT: A 769 LYS cc_start: 0.8497 (mmtp) cc_final: 0.7935 (mtmm) REVERT: A 811 LEU cc_start: 0.8119 (tp) cc_final: 0.7772 (tp) REVERT: A 971 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7690 (mt-10) REVERT: B 579 PHE cc_start: 0.6153 (OUTLIER) cc_final: 0.5211 (p90) REVERT: B 769 LYS cc_start: 0.8577 (mmtp) cc_final: 0.7983 (mtmm) REVERT: B 918 GLN cc_start: 0.7573 (tt0) cc_final: 0.7324 (tt0) REVERT: B 1056 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.8043 (ttt180) REVERT: B 1075 GLU cc_start: 0.7210 (pm20) cc_final: 0.6791 (pm20) REVERT: C 645 THR cc_start: 0.8571 (m) cc_final: 0.8293 (p) REVERT: C 714 MET cc_start: 0.8901 (ptm) cc_final: 0.8512 (ptt) REVERT: C 887 TYR cc_start: 0.8364 (t80) cc_final: 0.7977 (t80) outliers start: 43 outliers final: 34 residues processed: 229 average time/residue: 0.6981 time to fit residues: 268.0305 Evaluate side-chains 226 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 3.541 ------------------------------------------------------------------------------- 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 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 1056 ARG 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 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 271 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 205 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 237 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 23261 Z= 0.242 Angle : 0.482 5.413 31599 Z= 0.256 Chirality : 0.043 0.176 3613 Planarity : 0.003 0.038 4074 Dihedral : 3.988 33.282 3120 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.61 % Allowed : 14.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 2841 helix: 1.84 (0.20), residues: 658 sheet: 0.08 (0.21), residues: 606 loop : -0.99 (0.14), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 424 HIS 0.005 0.001 HIS B 54 PHE 0.015 0.001 PHE B 579 TYR 0.017 0.001 TYR A 623 ARG 0.002 0.000 ARG C 442 *********************** 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 238 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8431 (mt) REVERT: A 769 LYS cc_start: 0.8529 (mmtp) cc_final: 0.7966 (mtmm) REVERT: A 811 LEU cc_start: 0.8101 (tp) cc_final: 0.7781 (tp) REVERT: A 971 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7704 (mt-10) REVERT: B 579 PHE cc_start: 0.6181 (OUTLIER) cc_final: 0.5223 (p90) REVERT: B 769 LYS cc_start: 0.8557 (mmtp) cc_final: 0.7946 (mtmm) REVERT: B 918 GLN cc_start: 0.7557 (tt0) cc_final: 0.7297 (tt0) REVERT: B 1056 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7980 (ttt180) REVERT: B 1075 GLU cc_start: 0.7206 (pm20) cc_final: 0.6786 (pm20) REVERT: C 645 THR cc_start: 0.8561 (m) cc_final: 0.8283 (p) REVERT: C 887 TYR cc_start: 0.8383 (t80) cc_final: 0.7992 (t80) outliers start: 41 outliers final: 37 residues processed: 231 average time/residue: 0.7080 time to fit residues: 271.4650 Evaluate side-chains 230 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 3.715 ------------------------------------------------------------------------------- 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 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 1056 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 220 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN A1057 ASN ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 23261 Z= 0.228 Angle : 0.478 5.598 31599 Z= 0.254 Chirality : 0.043 0.174 3613 Planarity : 0.003 0.033 4074 Dihedral : 3.969 32.716 3120 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.65 % Allowed : 14.81 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 2841 helix: 1.91 (0.20), residues: 652 sheet: 0.08 (0.21), residues: 604 loop : -0.97 (0.14), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 424 HIS 0.004 0.001 HIS C 54 PHE 0.017 0.001 PHE B 579 TYR 0.014 0.001 TYR A 623 ARG 0.002 0.000 ARG B1022 *********************** 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: 42 poor density : 192 time to evaluate : 3.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8438 (mt) REVERT: A 769 LYS cc_start: 0.8545 (mmtp) cc_final: 0.7975 (mtmm) REVERT: A 811 LEU cc_start: 0.8124 (tp) cc_final: 0.7801 (tp) REVERT: A 971 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7757 (mt-10) REVERT: B 579 PHE cc_start: 0.6113 (OUTLIER) cc_final: 0.5205 (p90) REVERT: B 769 LYS cc_start: 0.8572 (mmtp) cc_final: 0.7961 (mtmm) REVERT: B 918 GLN cc_start: 0.7568 (tt0) cc_final: 0.7327 (tt0) REVERT: B 1056 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8013 (ttt180) REVERT: B 1075 GLU cc_start: 0.7144 (pm20) cc_final: 0.6732 (pm20) REVERT: C 645 THR cc_start: 0.8547 (m) cc_final: 0.8274 (p) REVERT: C 887 TYR cc_start: 0.8394 (t80) cc_final: 0.7995 (t80) outliers start: 42 outliers final: 39 residues processed: 226 average time/residue: 0.7230 time to fit residues: 273.0442 Evaluate side-chains 230 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 3.572 ------------------------------------------------------------------------------- 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 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 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 1056 ARG 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 255 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 205 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 260 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23261 Z= 0.180 Angle : 0.458 4.712 31599 Z= 0.241 Chirality : 0.043 0.170 3613 Planarity : 0.003 0.033 4074 Dihedral : 3.871 32.290 3120 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.50 % Allowed : 14.89 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 2841 helix: 2.01 (0.20), residues: 652 sheet: 0.14 (0.21), residues: 604 loop : -0.90 (0.14), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 424 HIS 0.003 0.001 HIS C 54 PHE 0.016 0.001 PHE B 579 TYR 0.013 0.001 TYR A1050 ARG 0.002 0.000 ARG B1022 *********************** 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 229 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 3.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8431 (mt) REVERT: A 769 LYS cc_start: 0.8508 (mmtp) cc_final: 0.7925 (mtmm) REVERT: A 811 LEU cc_start: 0.8110 (tp) cc_final: 0.7782 (tp) REVERT: A 971 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7762 (mt-10) REVERT: A 1116 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.6985 (tt) REVERT: B 579 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.5193 (p90) REVERT: B 769 LYS cc_start: 0.8593 (mmtp) cc_final: 0.7969 (mtmm) REVERT: B 918 GLN cc_start: 0.7560 (tt0) cc_final: 0.7312 (tt0) REVERT: B 1056 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8085 (ttt180) REVERT: B 1075 GLU cc_start: 0.7202 (pm20) cc_final: 0.6805 (pm20) REVERT: C 645 THR cc_start: 0.8542 (m) cc_final: 0.8273 (p) REVERT: C 887 TYR cc_start: 0.8399 (t80) cc_final: 0.8010 (t80) outliers start: 38 outliers final: 32 residues processed: 223 average time/residue: 0.7046 time to fit residues: 259.2471 Evaluate side-chains 224 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 3.774 ------------------------------------------------------------------------------- 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 641 GLU 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 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 1056 ARG 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 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 171 optimal weight: 0.9990 chunk 276 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 289 optimal weight: 0.9990 chunk 266 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23261 Z= 0.242 Angle : 0.479 4.700 31599 Z= 0.253 Chirality : 0.043 0.176 3613 Planarity : 0.003 0.034 4074 Dihedral : 3.947 32.172 3120 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.58 % Allowed : 14.81 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 2841 helix: 1.94 (0.20), residues: 652 sheet: 0.08 (0.21), residues: 607 loop : -0.95 (0.14), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 424 HIS 0.005 0.001 HIS A 54 PHE 0.017 0.001 PHE B 579 TYR 0.016 0.001 TYR A 623 ARG 0.002 0.000 ARG B 442 ********************** 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 232 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 3.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8460 (mt) REVERT: A 697 ILE cc_start: 0.8332 (pt) cc_final: 0.8048 (mt) REVERT: A 769 LYS cc_start: 0.8513 (mmtp) cc_final: 0.7943 (mtmm) REVERT: A 811 LEU cc_start: 0.8163 (tp) cc_final: 0.7836 (tp) REVERT: A 971 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7785 (mt-10) REVERT: B 579 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.5253 (p90) REVERT: B 769 LYS cc_start: 0.8605 (mmtp) cc_final: 0.7975 (mtmm) REVERT: B 918 GLN cc_start: 0.7583 (tt0) cc_final: 0.7319 (tt0) REVERT: B 1056 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7985 (ttt180) REVERT: B 1075 GLU cc_start: 0.7194 (pm20) cc_final: 0.6793 (pm20) REVERT: C 645 THR cc_start: 0.8534 (m) cc_final: 0.8260 (p) REVERT: C 887 TYR cc_start: 0.8396 (t80) cc_final: 0.7999 (t80) outliers start: 40 outliers final: 36 residues processed: 226 average time/residue: 0.7000 time to fit residues: 260.7332 Evaluate side-chains 228 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 3.397 ------------------------------------------------------------------------------- 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 641 GLU 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 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 1056 ARG 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 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 183 optimal weight: 0.0980 chunk 245 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 231 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 237 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 628 ASN ** 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 = 0.3512 r_free = 0.3512 target = 0.128928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111986 restraints weight = 83171.963| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.09 r_work: 0.3180 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23261 Z= 0.171 Angle : 0.454 4.229 31599 Z= 0.239 Chirality : 0.043 0.168 3613 Planarity : 0.003 0.034 4074 Dihedral : 3.847 31.853 3120 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.46 % Allowed : 15.01 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 2841 helix: 2.07 (0.20), residues: 652 sheet: 0.16 (0.21), residues: 604 loop : -0.87 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 424 HIS 0.003 0.001 HIS C 54 PHE 0.017 0.001 PHE B 579 TYR 0.013 0.001 TYR A1050 ARG 0.002 0.000 ARG B1022 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8613.67 seconds wall clock time: 156 minutes 48.95 seconds (9408.95 seconds total)