Starting phenix.real_space_refine on Fri Feb 6 10:44:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vhm_31999/02_2026/7vhm_31999.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vhm_31999/02_2026/7vhm_31999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vhm_31999/02_2026/7vhm_31999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vhm_31999/02_2026/7vhm_31999.map" model { file = "/net/cci-nas-00/data/ceres_data/7vhm_31999/02_2026/7vhm_31999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vhm_31999/02_2026/7vhm_31999.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 15966 2.51 5 N 4149 2.21 5 O 4740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24972 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8326 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 53, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'ARG:plan': 7, 'ASP:plan': 3, 'GLU:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "B" Number of atoms: 8326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8326 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 53, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'ARG:plan': 7, 'ASP:plan': 3, 'GLU:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 8320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8320 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 53, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 91 Planarities with less than four sites: {'ARG:plan': 7, 'ASP:plan': 3, 'GLU:plan': 8, 'TYR:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 101 Time building chain proxies: 6.15, per 1000 atoms: 0.25 Number of scatterers: 24972 At special positions: 0 Unit cell: (148.72, 149.76, 175.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 4740 8.00 N 4149 7.00 C 15966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.04 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 516 " distance=2.04 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 581 " distance=2.03 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 640 " distance=2.03 Simple disulfide: pdb=" SG CYS A 653 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 722 " - pdb=" SG CYS A 744 " distance=2.03 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS A1016 " - pdb=" SG CYS A1027 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 516 " distance=2.04 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 479 " distance=2.03 Simple disulfide: pdb=" SG CYS B 529 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 640 " distance=2.03 Simple disulfide: pdb=" SG CYS B 653 " - pdb=" SG CYS B 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 722 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B1016 " - pdb=" SG CYS B1027 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1110 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.02 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 516 " distance=2.04 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 479 " distance=2.03 Simple disulfide: pdb=" SG CYS C 529 " - pdb=" SG CYS C 581 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 640 " distance=2.03 Simple disulfide: pdb=" SG CYS C 653 " - pdb=" SG CYS C 662 " distance=2.03 Simple disulfide: pdb=" SG CYS C 722 " - pdb=" SG CYS C 744 " distance=2.02 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 733 " distance=2.03 Simple disulfide: pdb=" SG CYS C1016 " - pdb=" SG CYS C1027 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1110 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6060 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 55 sheets defined 24.1% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 285 through 294 Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 374 through 381 removed outlier: 4.113A pdb=" N ASN A 379 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 381 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.542A pdb=" N GLU A 610 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 611 " --> pdb=" O CYS A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 611' Processing helix chain 'A' and resid 722 through 727 Processing helix chain 'A' and resid 731 through 738 removed outlier: 3.565A pdb=" N LEU A 736 " --> pdb=" O GLU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 743 through 767 Processing helix chain 'A' and resid 800 through 809 removed outlier: 3.737A pdb=" N LYS A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 840 Processing helix chain 'A' and resid 850 through 868 removed outlier: 3.841A pdb=" N GLN A 856 " --> pdb=" O GLU A 852 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 867 " --> pdb=" O ALA A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 875 removed outlier: 4.046A pdb=" N ALA A 874 " --> pdb=" O TRP A 870 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 875 " --> pdb=" O THR A 871 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 870 through 875' Processing helix chain 'A' and resid 881 through 892 removed outlier: 3.567A pdb=" N ALA A 887 " --> pdb=" O ALA A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 903 through 923 Processing helix chain 'A' and resid 925 through 928 removed outlier: 3.658A pdb=" N ALA A 928 " --> pdb=" O THR A 925 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 925 through 928' Processing helix chain 'A' and resid 929 through 949 Processing helix chain 'A' and resid 950 through 952 No H-bonds generated for 'chain 'A' and resid 950 through 952' Processing helix chain 'A' and resid 960 through 966 removed outlier: 3.606A pdb=" N ILE A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 966 " --> pdb=" O ASN A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1017 removed outlier: 4.984A pdb=" N VAL A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLN A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1129 Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 328 through 334 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 374 through 381 removed outlier: 4.167A pdb=" N ASN B 379 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 607 through 611 removed outlier: 3.573A pdb=" N GLU B 610 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 611 " --> pdb=" O CYS B 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 607 through 611' Processing helix chain 'B' and resid 722 through 727 Processing helix chain 'B' and resid 731 through 738 removed outlier: 3.605A pdb=" N LEU B 736 " --> pdb=" O GLU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 741 No H-bonds generated for 'chain 'B' and resid 739 through 741' Processing helix chain 'B' and resid 742 through 767 removed outlier: 3.513A pdb=" N GLN B 746 " --> pdb=" O SER B 742 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 762 " --> pdb=" O GLN B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 809 removed outlier: 3.772A pdb=" N LYS B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 840 Processing helix chain 'B' and resid 850 through 868 removed outlier: 3.905A pdb=" N GLN B 856 " --> pdb=" O GLU B 852 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 859 " --> pdb=" O ALA B 855 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 867 " --> pdb=" O ALA B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 875 removed outlier: 4.182A pdb=" N ALA B 874 " --> pdb=" O TRP B 870 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 875 " --> pdb=" O THR B 871 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 870 through 875' Processing helix chain 'B' and resid 881 through 894 removed outlier: 3.575A pdb=" N ALA B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 893 " --> pdb=" O ARG B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 900 Processing helix chain 'B' and resid 903 through 923 Processing helix chain 'B' and resid 925 through 928 removed outlier: 3.654A pdb=" N ALA B 928 " --> pdb=" O THR B 925 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 925 through 928' Processing helix chain 'B' and resid 929 through 949 Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 960 through 965 removed outlier: 3.543A pdb=" N ILE B 964 " --> pdb=" O VAL B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 969 through 1017 removed outlier: 4.923A pdb=" N VAL B 975 " --> pdb=" O PRO B 971 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 1124 through 1129 Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 285 through 294 Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 374 through 381 removed outlier: 4.187A pdb=" N ASN C 379 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 381 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 398 Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 607 through 611 removed outlier: 3.562A pdb=" N GLU C 610 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 611 " --> pdb=" O CYS C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 611' Processing helix chain 'C' and resid 722 through 727 Processing helix chain 'C' and resid 731 through 738 removed outlier: 3.534A pdb=" N LEU C 736 " --> pdb=" O GLU C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 741 No H-bonds generated for 'chain 'C' and resid 739 through 741' Processing helix chain 'C' and resid 742 through 767 removed outlier: 3.623A pdb=" N GLN C 746 " --> pdb=" O SER C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 809 removed outlier: 3.648A pdb=" N LYS C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 840 Processing helix chain 'C' and resid 850 through 868 removed outlier: 3.827A pdb=" N GLN C 856 " --> pdb=" O GLU C 852 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C 867 " --> pdb=" O ALA C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 875 removed outlier: 4.089A pdb=" N ALA C 874 " --> pdb=" O TRP C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 893 removed outlier: 3.612A pdb=" N ALA C 887 " --> pdb=" O ALA C 883 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 893 " --> pdb=" O ARG C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 903 through 923 Processing helix chain 'C' and resid 925 through 928 removed outlier: 3.660A pdb=" N ALA C 928 " --> pdb=" O THR C 925 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 925 through 928' Processing helix chain 'C' and resid 929 through 949 Processing helix chain 'C' and resid 950 through 952 No H-bonds generated for 'chain 'C' and resid 950 through 952' Processing helix chain 'C' and resid 960 through 965 removed outlier: 3.597A pdb=" N ILE C 964 " --> pdb=" O VAL C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 1017 removed outlier: 4.947A pdb=" N VAL C 975 " --> pdb=" O PRO C 971 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN C 976 " --> pdb=" O GLU C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 1124 through 1129 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.882A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N ASN A 61 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR A 260 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 258 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 255 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 259 " --> pdb=" O TYR A 82 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 87 " --> pdb=" O ASN A 179 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 178 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 201 " --> pdb=" O LYS A 178 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 188 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE A 192 " --> pdb=" O ASP A 219 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP A 219 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE A 194 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N HIS A 198 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ALA A 213 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL A 36 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.699A pdb=" N GLY C 557 " --> pdb=" O ASP C 565 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.841A pdb=" N ASP A 278 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 107 through 110 removed outlier: 3.764A pdb=" N SER A 107 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 121 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A 159 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 302 through 307 removed outlier: 7.234A pdb=" N VAL A 586 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY A 585 " --> pdb=" O GLN A 604 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 315 through 316 removed outlier: 7.561A pdb=" N GLU A 315 " --> pdb=" O ASN A 531 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ASN A 533 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 539 " --> pdb=" O PHE A 532 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 347 through 349 removed outlier: 3.576A pdb=" N LYS A 347 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 388 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 386 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 422 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 352 through 353 removed outlier: 3.600A pdb=" N CYS A 516 " --> pdb=" O CYS A 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 443 through 445 Processing sheet with id=AB2, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AB3, first strand: chain 'A' and resid 564 through 566 removed outlier: 6.817A pdb=" N GLY A 557 " --> pdb=" O ASP A 565 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE A 556 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 644 through 645 removed outlier: 4.628A pdb=" N SER A 675 " --> pdb=" O GLN A 666 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN A 666 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.646A pdb=" N ILE A 661 " --> pdb=" O ILE A 657 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 685 through 686 removed outlier: 6.690A pdb=" N ALA A 685 " --> pdb=" O ILE B 772 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 695 through 697 removed outlier: 3.754A pdb=" N THR A1060 " --> pdb=" O SER A1081 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A1097 " --> pdb=" O VAL A1088 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN A1090 " --> pdb=" O GLU A1095 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLU A1095 " --> pdb=" O GLN A1090 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 701 through 712 removed outlier: 6.920A pdb=" N VAL A1049 " --> pdb=" O LEU A1033 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 701 through 712 Processing sheet with id=AC1, first strand: chain 'A' and resid 717 through 720 removed outlier: 4.294A pdb=" N LYS A 717 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 771 through 772 Processing sheet with id=AC3, first strand: chain 'A' and resid 1104 through 1106 Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.189A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N ASN B 61 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR B 260 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 258 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B 255 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 84 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY B 259 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 87 " --> pdb=" O ASN B 179 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS B 178 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE B 201 " --> pdb=" O LYS B 178 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 180 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 199 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE B 192 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP B 219 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE B 194 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N HIS B 198 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N ALA B 213 " --> pdb=" O HIS B 198 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL B 36 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.264A pdb=" N ASP B 53 " --> pdb=" O ARG B 264 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP B 278 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 107 through 110 removed outlier: 3.738A pdb=" N SER B 107 " --> pdb=" O CYS B 122 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL B 121 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE B 159 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 302 through 309 removed outlier: 3.557A pdb=" N TYR B 304 " --> pdb=" O VAL B 588 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL B 586 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN B 308 " --> pdb=" O GLY B 584 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY B 584 " --> pdb=" O ASN B 308 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY B 585 " --> pdb=" O GLN B 604 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 315 through 316 removed outlier: 7.616A pdb=" N GLU B 315 " --> pdb=" O ASN B 531 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ASN B 533 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.842A pdb=" N ASN B 345 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 390 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS B 347 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL B 386 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 422 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR B 371 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 352 through 353 removed outlier: 3.612A pdb=" N CYS B 516 " --> pdb=" O CYS B 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 443 through 445 Processing sheet with id=AD3, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AD4, first strand: chain 'B' and resid 564 through 567 removed outlier: 6.782A pdb=" N GLY B 557 " --> pdb=" O ASP B 565 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE B 556 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 644 through 645 removed outlier: 4.597A pdb=" N SER B 675 " --> pdb=" O GLN B 666 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN B 666 " --> pdb=" O SER B 675 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 656 through 658 removed outlier: 6.576A pdb=" N ILE B 661 " --> pdb=" O ILE B 657 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 685 through 686 removed outlier: 6.827A pdb=" N ALA B 685 " --> pdb=" O ILE C 772 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 695 through 697 removed outlier: 3.733A pdb=" N THR B1060 " --> pdb=" O SER B1081 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 701 through 712 removed outlier: 7.184A pdb=" N GLY B1043 " --> pdb=" O SER B1039 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N SER B1039 " --> pdb=" O GLY B1043 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B1045 " --> pdb=" O PRO B1037 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU B1047 " --> pdb=" O SER B1035 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER B1035 " --> pdb=" O LEU B1047 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL B1049 " --> pdb=" O LEU B1033 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 717 through 720 removed outlier: 4.253A pdb=" N LYS B 717 " --> pdb=" O LEU B 845 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1104 through 1106 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.178A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N ASN C 61 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR C 260 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA C 255 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR C 86 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 84 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 259 " --> pdb=" O TYR C 82 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 87 " --> pdb=" O ASN C 179 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS C 178 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE C 201 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE C 192 " --> pdb=" O ASP C 219 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP C 219 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE C 194 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS C 198 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N ALA C 213 " --> pdb=" O HIS C 198 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL C 36 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.692A pdb=" N ASP C 278 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE6, first strand: chain 'C' and resid 107 through 110 removed outlier: 3.792A pdb=" N SER C 107 " --> pdb=" O CYS C 122 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE C 119 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU C 160 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL C 121 " --> pdb=" O THR C 158 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN C 156 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLN C 125 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA C 154 " --> pdb=" O GLN C 125 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 302 through 307 removed outlier: 7.246A pdb=" N VAL C 586 " --> pdb=" O THR C 306 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY C 585 " --> pdb=" O GLN C 604 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 315 through 316 removed outlier: 7.517A pdb=" N GLU C 315 " --> pdb=" O ASN C 531 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASN C 533 " --> pdb=" O GLU C 315 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY C 539 " --> pdb=" O PHE C 532 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 347 through 349 removed outlier: 3.684A pdb=" N LYS C 347 " --> pdb=" O ALA C 388 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL C 386 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 422 " --> pdb=" O TYR C 371 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR C 371 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL C 424 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 369 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 367 " --> pdb=" O ALA C 426 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 352 through 353 removed outlier: 3.629A pdb=" N CYS C 516 " --> pdb=" O CYS C 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 443 through 445 Processing sheet with id=AF3, first strand: chain 'C' and resid 544 through 545 Processing sheet with id=AF4, first strand: chain 'C' and resid 644 through 645 removed outlier: 4.622A pdb=" N SER C 675 " --> pdb=" O GLN C 666 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN C 666 " --> pdb=" O SER C 675 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 656 through 658 removed outlier: 6.626A pdb=" N ILE C 661 " --> pdb=" O ILE C 657 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 695 through 697 removed outlier: 3.768A pdb=" N THR C1060 " --> pdb=" O SER C1081 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C1062 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE C1079 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C1097 " --> pdb=" O VAL C1088 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 701 through 712 removed outlier: 6.903A pdb=" N VAL C1049 " --> pdb=" O LEU C1033 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 701 through 712 Processing sheet with id=AF9, first strand: chain 'C' and resid 717 through 720 removed outlier: 4.325A pdb=" N LYS C 717 " --> pdb=" O LEU C 845 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1104 through 1106 856 hydrogen bonds defined for protein. 2358 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.84 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8049 1.35 - 1.47: 6475 1.47 - 1.60: 10888 1.60 - 1.72: 0 1.72 - 1.84: 147 Bond restraints: 25559 Sorted by residual: bond pdb=" CG LEU C 900 " pdb=" CD1 LEU C 900 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" CB CYS C 722 " pdb=" SG CYS C 722 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.78e+00 bond pdb=" CB PRO B 580 " pdb=" CG PRO B 580 " ideal model delta sigma weight residual 1.492 1.550 -0.058 5.00e-02 4.00e+02 1.34e+00 bond pdb=" CB CYS C 157 " pdb=" SG CYS C 157 " ideal model delta sigma weight residual 1.808 1.772 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" C LEU B 509 " pdb=" N HIS B 510 " ideal model delta sigma weight residual 1.332 1.317 0.015 1.40e-02 5.10e+03 1.17e+00 ... (remaining 25554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 34612 2.92 - 5.85: 205 5.85 - 8.77: 13 8.77 - 11.70: 2 11.70 - 14.62: 1 Bond angle restraints: 34833 Sorted by residual: angle pdb=" C TYR C 480 " pdb=" N PHE C 481 " pdb=" CA PHE C 481 " ideal model delta sigma weight residual 122.31 136.93 -14.62 2.34e+00 1.83e-01 3.90e+01 angle pdb=" C TYR B 480 " pdb=" N PHE B 481 " pdb=" CA PHE B 481 " ideal model delta sigma weight residual 122.31 133.98 -11.67 2.34e+00 1.83e-01 2.49e+01 angle pdb=" N GLY B1108 " pdb=" CA GLY B1108 " pdb=" C GLY B1108 " ideal model delta sigma weight residual 110.20 116.40 -6.20 1.32e+00 5.74e-01 2.20e+01 angle pdb=" N CYS A 423 " pdb=" CA CYS A 423 " pdb=" C CYS A 423 " ideal model delta sigma weight residual 108.24 113.27 -5.03 1.32e+00 5.74e-01 1.45e+01 angle pdb=" N CYS C 423 " pdb=" CA CYS C 423 " pdb=" C CYS C 423 " ideal model delta sigma weight residual 108.45 112.96 -4.51 1.26e+00 6.30e-01 1.28e+01 ... (remaining 34828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13757 17.99 - 35.99: 1154 35.99 - 53.98: 224 53.98 - 71.98: 49 71.98 - 89.97: 30 Dihedral angle restraints: 15214 sinusoidal: 5785 harmonic: 9429 Sorted by residual: dihedral pdb=" CB CYS B 529 " pdb=" SG CYS B 529 " pdb=" SG CYS B 581 " pdb=" CB CYS B 581 " ideal model delta sinusoidal sigma weight residual -86.00 -165.35 79.35 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS A 529 " pdb=" SG CYS A 529 " pdb=" SG CYS A 581 " pdb=" CB CYS A 581 " ideal model delta sinusoidal sigma weight residual -86.00 -164.56 78.56 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS C 529 " pdb=" SG CYS C 529 " pdb=" SG CYS C 581 " pdb=" CB CYS C 581 " ideal model delta sinusoidal sigma weight residual -86.00 -164.21 78.21 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 15211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2779 0.042 - 0.085: 863 0.085 - 0.127: 319 0.127 - 0.170: 21 0.170 - 0.212: 5 Chirality restraints: 3987 Sorted by residual: chirality pdb=" CB THR C 86 " pdb=" CA THR C 86 " pdb=" OG1 THR C 86 " pdb=" CG2 THR C 86 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB THR B 86 " pdb=" CA THR B 86 " pdb=" OG1 THR B 86 " pdb=" CG2 THR B 86 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" CB VAL A1078 " pdb=" CA VAL A1078 " pdb=" CG1 VAL A1078 " pdb=" CG2 VAL A1078 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.76e-01 ... (remaining 3984 not shown) Planarity restraints: 4511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 327 " 0.090 5.00e-02 4.00e+02 1.37e-01 3.00e+01 pdb=" N PRO C 328 " -0.237 5.00e-02 4.00e+02 pdb=" CA PRO C 328 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO C 328 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 511 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO B 512 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 512 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 512 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 511 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.73e+00 pdb=" N PRO C 512 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 512 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 512 " -0.039 5.00e-02 4.00e+02 ... (remaining 4508 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 590 2.68 - 3.23: 24574 3.23 - 3.79: 37411 3.79 - 4.34: 52876 4.34 - 4.90: 88107 Nonbonded interactions: 203558 Sorted by model distance: nonbonded pdb=" OE1 GLU C 803 " pdb=" OG SER C1039 " model vdw 2.124 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 265 " model vdw 2.128 3.040 nonbonded pdb=" OE1 GLU A 803 " pdb=" OG SER A1039 " model vdw 2.143 3.040 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 265 " model vdw 2.146 3.040 nonbonded pdb=" OE1 GLN A 52 " pdb=" OG1 THR A 265 " model vdw 2.157 3.040 ... (remaining 203553 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 14 through 147 or (resid 148 through 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 1131)) selection = (chain 'B' and (resid 14 through 147 or (resid 148 through 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 1131)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.210 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: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.480 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 0.058 25601 Z= 0.167 Angle : 0.665 14.622 34917 Z= 0.380 Chirality : 0.046 0.212 3987 Planarity : 0.005 0.137 4511 Dihedral : 14.391 89.974 9028 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.14), residues: 3219 helix: -0.01 (0.20), residues: 669 sheet: -1.99 (0.22), residues: 603 loop : -2.81 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 348 TYR 0.017 0.001 TYR C 342 PHE 0.041 0.002 PHE B 890 TRP 0.024 0.002 TRP A 870 HIS 0.011 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00371 (25559) covalent geometry : angle 0.66105 (34833) SS BOND : bond 0.00508 ( 42) SS BOND : angle 1.61834 ( 84) hydrogen bonds : bond 0.21045 ( 832) hydrogen bonds : angle 9.07694 ( 2358) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: C 886 MET cc_start: 0.7789 (tpp) cc_final: 0.7557 (mmt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1535 time to fit residues: 59.0391 Evaluate side-chains 176 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.0770 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0010 chunk 298 optimal weight: 1.9990 overall best weight: 1.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A1097 GLN B 439 ASN B 597 ASN B 885 GLN C 179 ASN C 439 ASN C 885 GLN C1109 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.192746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.149295 restraints weight = 30112.469| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.93 r_work: 0.3240 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25601 Z= 0.167 Angle : 0.602 8.826 34917 Z= 0.316 Chirality : 0.046 0.164 3987 Planarity : 0.005 0.093 4511 Dihedral : 5.020 21.312 3456 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.76 % Allowed : 5.62 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.14), residues: 3219 helix: 0.54 (0.21), residues: 639 sheet: -1.70 (0.22), residues: 624 loop : -2.46 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 264 TYR 0.023 0.001 TYR A1051 PHE 0.050 0.001 PHE C 329 TRP 0.030 0.002 TRP A 95 HIS 0.008 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00402 (25559) covalent geometry : angle 0.59749 (34833) SS BOND : bond 0.00462 ( 42) SS BOND : angle 1.57277 ( 84) hydrogen bonds : bond 0.04812 ( 832) hydrogen bonds : angle 6.40458 ( 2358) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.904 Fit side-chains REVERT: A 95 TRP cc_start: 0.6533 (m-90) cc_final: 0.6326 (m-90) REVERT: A 278 ASP cc_start: 0.7322 (m-30) cc_final: 0.7083 (m-30) REVERT: A 919 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8501 (tm-30) REVERT: B 131 PHE cc_start: 0.6019 (p90) cc_final: 0.5628 (p90) REVERT: B 568 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7181 (ptm160) outliers start: 21 outliers final: 17 residues processed: 215 average time/residue: 0.1386 time to fit residues: 51.4070 Evaluate side-chains 187 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1097 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 722 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 236 optimal weight: 8.9990 chunk 181 optimal weight: 0.3980 chunk 173 optimal weight: 0.2980 chunk 280 optimal weight: 0.0070 chunk 98 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 153 optimal weight: 10.0000 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 GLN B 597 ASN B 674 GLN B 758 GLN C 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.194376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.151415 restraints weight = 30303.064| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.83 r_work: 0.3274 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25601 Z= 0.126 Angle : 0.549 9.036 34917 Z= 0.287 Chirality : 0.044 0.154 3987 Planarity : 0.004 0.082 4511 Dihedral : 4.761 20.817 3456 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.02 % Allowed : 8.67 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.15), residues: 3219 helix: 0.87 (0.21), residues: 636 sheet: -1.52 (0.21), residues: 654 loop : -2.32 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 348 TYR 0.021 0.001 TYR C1051 PHE 0.014 0.001 PHE A1105 TRP 0.018 0.001 TRP B 64 HIS 0.007 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00299 (25559) covalent geometry : angle 0.54565 (34833) SS BOND : bond 0.00378 ( 42) SS BOND : angle 1.29543 ( 84) hydrogen bonds : bond 0.04140 ( 832) hydrogen bonds : angle 5.87158 ( 2358) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 919 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8269 (tm-30) REVERT: B 131 PHE cc_start: 0.5718 (p90) cc_final: 0.5379 (p90) REVERT: B 278 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.7082 (m-30) REVERT: B 568 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7300 (ptm160) REVERT: C 41 LYS cc_start: 0.8068 (mmtt) cc_final: 0.7714 (mmtm) outliers start: 28 outliers final: 18 residues processed: 211 average time/residue: 0.1472 time to fit residues: 52.6521 Evaluate side-chains 197 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 722 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 152 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 259 optimal weight: 0.0970 chunk 221 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.190597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146541 restraints weight = 30026.390| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.91 r_work: 0.3203 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 25601 Z= 0.249 Angle : 0.615 10.526 34917 Z= 0.317 Chirality : 0.047 0.170 3987 Planarity : 0.004 0.069 4511 Dihedral : 4.924 20.165 3456 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.56 % Allowed : 9.83 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.14), residues: 3219 helix: 0.49 (0.21), residues: 657 sheet: -1.55 (0.21), residues: 630 loop : -2.34 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 348 TYR 0.027 0.002 TYR B 256 PHE 0.026 0.002 PHE B 890 TRP 0.026 0.002 TRP B 64 HIS 0.007 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00613 (25559) covalent geometry : angle 0.61076 (34833) SS BOND : bond 0.00419 ( 42) SS BOND : angle 1.54950 ( 84) hydrogen bonds : bond 0.04786 ( 832) hydrogen bonds : angle 5.89162 ( 2358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.904 Fit side-chains REVERT: A 131 PHE cc_start: 0.5621 (p90) cc_final: 0.5187 (p90) REVERT: B 131 PHE cc_start: 0.5862 (p90) cc_final: 0.5534 (p90) REVERT: B 568 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7049 (ptm160) outliers start: 43 outliers final: 33 residues processed: 222 average time/residue: 0.1436 time to fit residues: 54.8436 Evaluate side-chains 213 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 722 CYS Chi-restraints excluded: chain C residue 769 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 85 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 217 optimal weight: 7.9990 chunk 311 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 122 optimal weight: 0.0570 chunk 59 optimal weight: 4.9990 chunk 108 optimal weight: 0.0070 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 763 GLN ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.195652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144475 restraints weight = 30102.793| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.11 r_work: 0.3227 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25601 Z= 0.107 Angle : 0.533 10.639 34917 Z= 0.275 Chirality : 0.043 0.152 3987 Planarity : 0.004 0.062 4511 Dihedral : 4.554 20.174 3456 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.56 % Allowed : 10.81 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.15), residues: 3219 helix: 1.10 (0.21), residues: 639 sheet: -1.34 (0.21), residues: 660 loop : -2.15 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 348 TYR 0.020 0.001 TYR C1051 PHE 0.016 0.001 PHE B 32 TRP 0.017 0.001 TRP B 64 HIS 0.006 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00247 (25559) covalent geometry : angle 0.53021 (34833) SS BOND : bond 0.00365 ( 42) SS BOND : angle 1.23909 ( 84) hydrogen bonds : bond 0.03751 ( 832) hydrogen bonds : angle 5.48199 ( 2358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 201 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7602 (t60) cc_final: 0.6950 (t60) REVERT: A 233 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6669 (tt) REVERT: B 131 PHE cc_start: 0.5758 (p90) cc_final: 0.5456 (p90) REVERT: B 278 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6975 (m-30) REVERT: C 41 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7757 (mmtm) REVERT: C 278 ASP cc_start: 0.7372 (m-30) cc_final: 0.7059 (m-30) outliers start: 43 outliers final: 24 residues processed: 232 average time/residue: 0.1475 time to fit residues: 58.2445 Evaluate side-chains 211 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 722 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 77 optimal weight: 0.5980 chunk 238 optimal weight: 10.0000 chunk 311 optimal weight: 0.3980 chunk 188 optimal weight: 0.9990 chunk 247 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 218 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 chunk 233 optimal weight: 0.0770 chunk 82 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** C 72 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 = 0.4211 r_free = 0.4211 target = 0.196094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.145366 restraints weight = 30200.162| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.09 r_work: 0.3234 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25601 Z= 0.109 Angle : 0.521 10.901 34917 Z= 0.268 Chirality : 0.043 0.169 3987 Planarity : 0.004 0.056 4511 Dihedral : 4.383 19.848 3456 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.85 % Allowed : 10.96 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.15), residues: 3219 helix: 1.24 (0.21), residues: 639 sheet: -1.19 (0.21), residues: 657 loop : -2.09 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 348 TYR 0.020 0.001 TYR C1051 PHE 0.013 0.001 PHE A 32 TRP 0.018 0.001 TRP A 95 HIS 0.006 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00259 (25559) covalent geometry : angle 0.51845 (34833) SS BOND : bond 0.00318 ( 42) SS BOND : angle 1.16137 ( 84) hydrogen bonds : bond 0.03685 ( 832) hydrogen bonds : angle 5.32005 ( 2358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7608 (t60) cc_final: 0.6815 (t60) REVERT: A 233 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6598 (tt) REVERT: B 278 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7038 (m-30) REVERT: C 41 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7611 (mmtm) REVERT: C 278 ASP cc_start: 0.7346 (m-30) cc_final: 0.7094 (m-30) REVERT: C 941 GLN cc_start: 0.8827 (tt0) cc_final: 0.8368 (tp40) outliers start: 51 outliers final: 34 residues processed: 235 average time/residue: 0.1429 time to fit residues: 57.5163 Evaluate side-chains 222 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1128 GLU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 1111 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 193 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 274 optimal weight: 0.7980 chunk 144 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 273 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN ** C 72 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 = 0.4197 r_free = 0.4197 target = 0.194746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.142925 restraints weight = 30131.668| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.04 r_work: 0.3203 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25601 Z= 0.147 Angle : 0.539 11.121 34917 Z= 0.278 Chirality : 0.044 0.287 3987 Planarity : 0.004 0.053 4511 Dihedral : 4.429 19.119 3456 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.96 % Allowed : 11.90 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.15), residues: 3219 helix: 1.14 (0.21), residues: 639 sheet: -1.37 (0.20), residues: 693 loop : -2.04 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 348 TYR 0.019 0.001 TYR B 256 PHE 0.025 0.001 PHE A 32 TRP 0.020 0.001 TRP B 64 HIS 0.006 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00359 (25559) covalent geometry : angle 0.53618 (34833) SS BOND : bond 0.00358 ( 42) SS BOND : angle 1.32164 ( 84) hydrogen bonds : bond 0.03985 ( 832) hydrogen bonds : angle 5.38702 ( 2358) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6643 (tt) REVERT: B 278 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.7034 (m-30) REVERT: C 41 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7688 (mmtm) REVERT: C 1129 LEU cc_start: 0.7788 (mp) cc_final: 0.7554 (mt) outliers start: 54 outliers final: 40 residues processed: 233 average time/residue: 0.1416 time to fit residues: 56.9950 Evaluate side-chains 222 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1128 GLU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1111 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 77 optimal weight: 0.8980 chunk 298 optimal weight: 0.9980 chunk 84 optimal weight: 0.0570 chunk 160 optimal weight: 7.9990 chunk 271 optimal weight: 0.9980 chunk 315 optimal weight: 0.9980 chunk 257 optimal weight: 5.9990 chunk 314 optimal weight: 3.9990 chunk 152 optimal weight: 30.0000 chunk 223 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.196219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148256 restraints weight = 30051.895| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.77 r_work: 0.3284 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25601 Z= 0.114 Angle : 0.521 11.084 34917 Z= 0.268 Chirality : 0.043 0.272 3987 Planarity : 0.004 0.052 4511 Dihedral : 4.317 19.216 3456 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.56 % Allowed : 12.37 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.15), residues: 3219 helix: 1.26 (0.21), residues: 642 sheet: -1.29 (0.20), residues: 693 loop : -1.98 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 348 TYR 0.019 0.001 TYR C1051 PHE 0.019 0.001 PHE B 839 TRP 0.019 0.001 TRP B 64 HIS 0.006 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00275 (25559) covalent geometry : angle 0.51781 (34833) SS BOND : bond 0.00307 ( 42) SS BOND : angle 1.25939 ( 84) hydrogen bonds : bond 0.03668 ( 832) hydrogen bonds : angle 5.24654 ( 2358) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6551 (tt) REVERT: A 1126 GLN cc_start: 0.7582 (tp40) cc_final: 0.7349 (mm110) REVERT: B 278 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6997 (m-30) REVERT: B 551 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6748 (mp) REVERT: C 329 PHE cc_start: 0.7521 (m-80) cc_final: 0.7293 (m-80) outliers start: 43 outliers final: 35 residues processed: 230 average time/residue: 0.1439 time to fit residues: 56.2087 Evaluate side-chains 223 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 1111 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 192 optimal weight: 1.9990 chunk 316 optimal weight: 0.9990 chunk 256 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 127 optimal weight: 0.0870 chunk 98 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 275 optimal weight: 6.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.195509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.144035 restraints weight = 30074.366| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.11 r_work: 0.3237 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25601 Z= 0.125 Angle : 0.526 11.261 34917 Z= 0.270 Chirality : 0.044 0.255 3987 Planarity : 0.004 0.050 4511 Dihedral : 4.302 18.754 3456 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.81 % Allowed : 12.08 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.15), residues: 3219 helix: 1.25 (0.21), residues: 642 sheet: -1.34 (0.20), residues: 714 loop : -1.95 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 348 TYR 0.019 0.001 TYR C1051 PHE 0.021 0.001 PHE B 83 TRP 0.026 0.002 TRP C 95 HIS 0.006 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00304 (25559) covalent geometry : angle 0.52282 (34833) SS BOND : bond 0.00348 ( 42) SS BOND : angle 1.27005 ( 84) hydrogen bonds : bond 0.03764 ( 832) hydrogen bonds : angle 5.23485 ( 2358) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 191 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6608 (tt) REVERT: A 329 PHE cc_start: 0.7812 (m-80) cc_final: 0.7111 (m-80) REVERT: A 1126 GLN cc_start: 0.7576 (tp40) cc_final: 0.7362 (mm110) REVERT: B 278 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7064 (m-30) REVERT: C 329 PHE cc_start: 0.7589 (m-80) cc_final: 0.7132 (m-80) outliers start: 50 outliers final: 42 residues processed: 229 average time/residue: 0.1446 time to fit residues: 56.9806 Evaluate side-chains 230 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 174 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 280 optimal weight: 0.9980 chunk 122 optimal weight: 0.0010 chunk 169 optimal weight: 0.7980 chunk 268 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 chunk 179 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 282 optimal weight: 0.8980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 758 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.197194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.155546 restraints weight = 30102.391| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.77 r_work: 0.3318 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25601 Z= 0.103 Angle : 0.516 11.164 34917 Z= 0.265 Chirality : 0.043 0.247 3987 Planarity : 0.004 0.049 4511 Dihedral : 4.206 18.835 3456 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.63 % Allowed : 12.34 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.15), residues: 3219 helix: 1.44 (0.21), residues: 645 sheet: -1.24 (0.20), residues: 696 loop : -1.87 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 348 TYR 0.019 0.001 TYR C1051 PHE 0.020 0.001 PHE B 83 TRP 0.021 0.001 TRP C 95 HIS 0.007 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00243 (25559) covalent geometry : angle 0.51318 (34833) SS BOND : bond 0.00321 ( 42) SS BOND : angle 1.13796 ( 84) hydrogen bonds : bond 0.03523 ( 832) hydrogen bonds : angle 5.12694 ( 2358) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6536 (tt) REVERT: A 329 PHE cc_start: 0.7864 (m-80) cc_final: 0.7244 (m-80) REVERT: A 941 GLN cc_start: 0.8829 (tt0) cc_final: 0.8478 (tp-100) REVERT: A 1126 GLN cc_start: 0.7703 (tp40) cc_final: 0.7470 (mm110) REVERT: C 233 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7307 (tt) REVERT: C 329 PHE cc_start: 0.7611 (m-80) cc_final: 0.7112 (m-80) REVERT: C 941 GLN cc_start: 0.8888 (tt0) cc_final: 0.8516 (tp40) outliers start: 45 outliers final: 39 residues processed: 243 average time/residue: 0.1418 time to fit residues: 58.8281 Evaluate side-chains 237 residues out of total 2823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 1111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 90 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 292 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 257 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 GLN ** C 72 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 = 0.4208 r_free = 0.4208 target = 0.195795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.146716 restraints weight = 30140.019| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.82 r_work: 0.3268 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25601 Z= 0.139 Angle : 0.535 11.205 34917 Z= 0.274 Chirality : 0.044 0.237 3987 Planarity : 0.004 0.048 4511 Dihedral : 4.267 18.704 3456 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.67 % Allowed : 12.59 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.15), residues: 3219 helix: 1.40 (0.21), residues: 639 sheet: -1.06 (0.21), residues: 651 loop : -1.93 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 348 TYR 0.019 0.001 TYR C1051 PHE 0.018 0.001 PHE B 83 TRP 0.020 0.002 TRP B 64 HIS 0.007 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00341 (25559) covalent geometry : angle 0.53191 (34833) SS BOND : bond 0.00344 ( 42) SS BOND : angle 1.26749 ( 84) hydrogen bonds : bond 0.03803 ( 832) hydrogen bonds : angle 5.18886 ( 2358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7183.53 seconds wall clock time: 123 minutes 54.17 seconds (7434.17 seconds total)