Starting phenix.real_space_refine on Tue Aug 26 01:29:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q5y_18180/08_2025/8q5y_18180.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q5y_18180/08_2025/8q5y_18180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8q5y_18180/08_2025/8q5y_18180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q5y_18180/08_2025/8q5y_18180.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q5y_18180/08_2025/8q5y_18180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q5y_18180/08_2025/8q5y_18180.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4615 atoms to isotropic. 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 126 5.16 5 C 18291 2.51 5 N 4777 2.21 5 O 5495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28689 Number of models: 1 Model: "" Number of chains: 9 Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "R" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 896 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "G" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 896 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "H" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 778 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "D" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "E" Number of atoms: 7818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7818 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 52, 'TRANS': 948} Chain breaks: 8 Chain: "C" Number of atoms: 7978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7978 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 966} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "B" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 902 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Time building chain proxies: 5.47, per 1000 atoms: 0.19 Number of scatterers: 28689 At special positions: 0 Unit cell: (134.33, 156.55, 209.07, 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 126 16.00 O 5495 8.00 N 4777 7.00 C 18291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.02 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.02 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.04 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.02 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.02 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.02 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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: 2.26 Conformation dependent library (CDL) restraints added in 918.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6856 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 63 sheets defined 21.6% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 removed outlier: 3.566A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 372 removed outlier: 3.880A pdb=" N LEU D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 408 removed outlier: 3.657A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 405 through 408' Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 757 removed outlier: 3.803A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR D 756 " --> pdb=" O LEU D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.616A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 891 removed outlier: 3.530A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 Processing helix chain 'D' and resid 912 through 919 removed outlier: 4.044A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1032 Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 3.908A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.575A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 372 removed outlier: 3.822A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 408 removed outlier: 3.919A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 405 through 408' Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 757 removed outlier: 3.850A pdb=" N GLN E 755 " --> pdb=" O ASN E 751 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR E 756 " --> pdb=" O LEU E 752 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY E 757 " --> pdb=" O LEU E 753 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.608A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 891 removed outlier: 3.609A pdb=" N ALA E 890 " --> pdb=" O TRP E 886 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 912 through 919 removed outlier: 3.724A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.632A pdb=" N VAL E 952 " --> pdb=" O LEU E 948 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 3.727A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG E 995 " --> pdb=" O VAL E 991 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1147 removed outlier: 4.054A pdb=" N GLU E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.810A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.843A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.852A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.589A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.048A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.738A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.717A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.726A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.012A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.793A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 44 through 49 removed outlier: 6.706A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'R' and resid 58 through 60 removed outlier: 4.920A pdb=" N TRP R 47 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 58 through 60 removed outlier: 4.920A pdb=" N TRP R 47 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.598A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE G 50 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE G 34 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG G 98 " --> pdb=" O SER G 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.598A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE G 50 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE G 34 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.568A pdb=" N ARG H 24 " --> pdb=" O THR H 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.435A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 28 through 30 removed outlier: 8.330A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU D 96 " --> pdb=" O ASN D 188 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASN D 188 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 197 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 224 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N HIS D 207 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N ALA D 222 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB4, first strand: chain 'D' and resid 48 through 55 removed outlier: 4.165A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 84 through 85 removed outlier: 5.637A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.324A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 325 through 328 removed outlier: 6.602A pdb=" N ILE D 326 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.953A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN D 394 " --> pdb=" O GLU D 516 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR D 430 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AC1, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.725A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.580A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 702 through 704 Processing sheet with id=AC4, first strand: chain 'D' and resid 711 through 715 Processing sheet with id=AC5, first strand: chain 'D' and resid 718 through 728 removed outlier: 6.051A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.414A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 787 through 790 Processing sheet with id=AC8, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AC9, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AD1, first strand: chain 'E' and resid 28 through 30 removed outlier: 8.930A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE E 203 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL E 227 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N HIS E 207 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N LEU E 223 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 48 through 55 removed outlier: 3.789A pdb=" N ASP E 53 " --> pdb=" O ARG E 273 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.917A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.021A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 118 through 122 Processing sheet with id=AD6, first strand: chain 'E' and resid 311 through 319 removed outlier: 7.243A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 325 through 328 removed outlier: 3.547A pdb=" N VAL E 539 " --> pdb=" O GLY E 550 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AD9, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.581A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.625A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 702 through 704 Processing sheet with id=AE4, first strand: chain 'E' and resid 711 through 715 removed outlier: 3.512A pdb=" N ILE E 712 " --> pdb=" O PHE E1075 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 718 through 728 removed outlier: 5.891A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.314A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.131A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.039A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.786A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.737A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.177A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.137A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.484A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF7, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.682A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.695A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE C 666 " --> pdb=" O ILE C 670 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.824A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.019A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.405A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG4, first strand: chain 'A' and resid 4 through 6 removed outlier: 3.714A pdb=" N THR A 5 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A 24 " --> pdb=" O THR A 5 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.748A pdb=" N ARG A 53 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 102 " --> pdb=" O TYR A 86 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.527A pdb=" N VAL B 5 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.527A pdb=" N VAL B 5 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 11 through 12 removed outlier: 7.378A pdb=" N PHE B 34 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ILE B 50 " --> pdb=" O PHE B 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS B 59 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 11 through 12 1207 hydrogen bonds defined for protein. 3330 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: 6.46 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 8302 1.34 - 1.47: 8234 1.47 - 1.61: 12648 1.61 - 1.74: 3 1.74 - 1.88: 156 Bond restraints: 29343 Sorted by residual: bond pdb=" N PRO E 942 " pdb=" CD PRO E 942 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.93e+01 bond pdb=" N PRO C 942 " pdb=" CD PRO C 942 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.68e+01 bond pdb=" N VAL L 91 " pdb=" CA VAL L 91 " ideal model delta sigma weight residual 1.459 1.496 -0.037 9.10e-03 1.21e+04 1.66e+01 bond pdb=" N PRO E 944 " pdb=" CD PRO E 944 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.54e+01 bond pdb=" N PRO C 944 " pdb=" CD PRO C 944 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.53e+01 ... (remaining 29338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 38801 2.80 - 5.60: 989 5.60 - 8.40: 100 8.40 - 11.20: 16 11.20 - 14.00: 16 Bond angle restraints: 39922 Sorted by residual: angle pdb=" CA PRO E 942 " pdb=" N PRO E 942 " pdb=" CD PRO E 942 " ideal model delta sigma weight residual 112.00 98.85 13.15 1.40e+00 5.10e-01 8.82e+01 angle pdb=" CA PRO E 944 " pdb=" N PRO E 944 " pdb=" CD PRO E 944 " ideal model delta sigma weight residual 112.00 98.90 13.10 1.40e+00 5.10e-01 8.76e+01 angle pdb=" CA PRO E 899 " pdb=" N PRO E 899 " pdb=" CD PRO E 899 " ideal model delta sigma weight residual 112.00 98.93 13.07 1.40e+00 5.10e-01 8.72e+01 angle pdb=" CA PRO C 944 " pdb=" N PRO C 944 " pdb=" CD PRO C 944 " ideal model delta sigma weight residual 112.00 99.17 12.83 1.40e+00 5.10e-01 8.40e+01 angle pdb=" CA PRO C 942 " pdb=" N PRO C 942 " pdb=" CD PRO C 942 " ideal model delta sigma weight residual 112.00 99.21 12.79 1.40e+00 5.10e-01 8.35e+01 ... (remaining 39917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 15596 17.94 - 35.89: 1503 35.89 - 53.83: 270 53.83 - 71.77: 59 71.77 - 89.71: 30 Dihedral angle restraints: 17458 sinusoidal: 6779 harmonic: 10679 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -23.28 -62.72 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CB CYS D 738 " pdb=" SG CYS D 738 " pdb=" SG CYS D 760 " pdb=" CB CYS D 760 " ideal model delta sinusoidal sigma weight residual 93.00 128.89 -35.89 1 1.00e+01 1.00e-02 1.82e+01 dihedral pdb=" CB CYS E 738 " pdb=" SG CYS E 738 " pdb=" SG CYS E 760 " pdb=" CB CYS E 760 " ideal model delta sinusoidal sigma weight residual 93.00 128.29 -35.29 1 1.00e+01 1.00e-02 1.76e+01 ... (remaining 17455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 4246 0.127 - 0.254: 264 0.254 - 0.381: 9 0.381 - 0.508: 2 0.508 - 0.635: 3 Chirality restraints: 4524 Sorted by residual: chirality pdb=" CB ILE E 101 " pdb=" CA ILE E 101 " pdb=" CG1 ILE E 101 " pdb=" CG2 ILE E 101 " both_signs ideal model delta sigma weight residual False 2.64 2.01 0.63 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CG LEU H 33 " pdb=" CB LEU H 33 " pdb=" CD1 LEU H 33 " pdb=" CD2 LEU H 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.81e+00 chirality pdb=" CB ILE E 285 " pdb=" CA ILE E 285 " pdb=" CG1 ILE E 285 " pdb=" CG2 ILE E 285 " both_signs ideal model delta sigma weight residual False 2.64 2.05 0.59 2.00e-01 2.50e+01 8.80e+00 ... (remaining 4521 not shown) Planarity restraints: 5173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 886 " 0.040 2.00e-02 2.50e+03 4.80e-02 5.76e+01 pdb=" CG TRP E 886 " -0.121 2.00e-02 2.50e+03 pdb=" CD1 TRP E 886 " 0.078 2.00e-02 2.50e+03 pdb=" CD2 TRP E 886 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP E 886 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP E 886 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 886 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 886 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 886 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP E 886 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 943 " 0.116 5.00e-02 4.00e+02 1.63e-01 4.26e+01 pdb=" N PRO E 944 " -0.282 5.00e-02 4.00e+02 pdb=" CA PRO E 944 " 0.088 5.00e-02 4.00e+02 pdb=" CD PRO E 944 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 943 " 0.115 5.00e-02 4.00e+02 1.62e-01 4.20e+01 pdb=" N PRO D 944 " -0.280 5.00e-02 4.00e+02 pdb=" CA PRO D 944 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO D 944 " 0.077 5.00e-02 4.00e+02 ... (remaining 5170 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 30 2.44 - 3.05: 16709 3.05 - 3.67: 44663 3.67 - 4.28: 68414 4.28 - 4.90: 112485 Nonbonded interactions: 242301 Sorted by model distance: nonbonded pdb=" O GLN E 804 " pdb=" CD PRO E 817 " model vdw 1.820 3.440 nonbonded pdb=" O GLN C 804 " pdb=" CD PRO C 817 " model vdw 1.924 3.440 nonbonded pdb=" O GLN D 804 " pdb=" CD PRO D 817 " model vdw 1.950 3.440 nonbonded pdb=" OD1 ASP G 104 " pdb=" NH2 ARG E 346 " model vdw 2.279 3.120 nonbonded pdb=" OG1 THR C 645 " pdb=" O GLY C 648 " model vdw 2.285 3.040 ... (remaining 242296 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 1 through 104) selection = chain 'H' selection = (chain 'L' and resid 1 through 104) } ncs_group { reference = (chain 'B' and resid 1 through 115) selection = chain 'G' selection = chain 'R' } ncs_group { reference = (chain 'C' and (resid 27 through 526 or resid 528 through 620 or resid 641 throu \ gh 1147)) selection = (chain 'D' and (resid 27 through 526 or resid 528 through 1147)) selection = chain 'E' } 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: 8.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 26.080 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 : 0.006 0.092 29388 Z= 0.327 Angle : 1.071 14.001 40012 Z= 0.631 Chirality : 0.068 0.635 4524 Planarity : 0.010 0.163 5173 Dihedral : 14.679 89.713 10467 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.48 % Favored : 97.46 % Rotamer: Outliers : 0.34 % Allowed : 1.22 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.13), residues: 3627 helix: 3.18 (0.18), residues: 682 sheet: 0.91 (0.16), residues: 926 loop : -0.06 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 34 TYR 0.059 0.003 TYR L 86 PHE 0.101 0.003 PHE C 906 TRP 0.121 0.004 TRP E 886 HIS 0.013 0.003 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00631 (29343) covalent geometry : angle 1.06425 (39922) SS BOND : bond 0.00567 ( 45) SS BOND : angle 2.79241 ( 90) hydrogen bonds : bond 0.18836 ( 1170) hydrogen bonds : angle 8.62053 ( 3330) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 467 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 VAL cc_start: 0.7522 (OUTLIER) cc_final: 0.7167 (m) REVERT: D 577 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7428 (ttm110) REVERT: D 814 LYS cc_start: 0.7007 (tttm) cc_final: 0.6636 (ttpp) REVERT: D 1019 ARG cc_start: 0.8095 (ttp-110) cc_final: 0.7892 (ttp-110) REVERT: E 129 LYS cc_start: 0.6795 (OUTLIER) cc_final: 0.6571 (pptt) REVERT: C 565 PHE cc_start: 0.6385 (m-80) cc_final: 0.5857 (m-80) outliers start: 11 outliers final: 1 residues processed: 478 average time/residue: 0.6210 time to fit residues: 347.4256 Evaluate side-chains 293 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 290 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 131 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** R 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS G 82 GLN D 188 ASN D 196 ASN D 388 ASN D 448 ASN D 450 ASN D 498 GLN ** D 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 ASN D 978 ASN D1002 GLN E 354 ASN E 607 GLN E 710 ASN E 751 ASN E 755 GLN E 779 GLN E 804 GLN E 901 GLN E 907 ASN E1010 GLN E1101 HIS C 30 ASN C 61 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 616 ASN C 641 ASN C 703 ASN C 804 GLN C 914 ASN C 926 GLN C 935 GLN C 954 GLN C1002 GLN C1010 GLN ** B 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.219650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.184919 restraints weight = 27122.433| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.53 r_work: 0.3796 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 29388 Z= 0.180 Angle : 0.615 9.060 40012 Z= 0.338 Chirality : 0.047 0.184 4524 Planarity : 0.005 0.071 5173 Dihedral : 4.785 33.794 3953 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.75 % Allowed : 9.69 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.13), residues: 3627 helix: 2.52 (0.18), residues: 691 sheet: 1.01 (0.17), residues: 893 loop : -0.09 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 454 TYR 0.035 0.002 TYR C 200 PHE 0.026 0.002 PHE C 906 TRP 0.028 0.002 TRP E 886 HIS 0.008 0.002 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.00414 (29343) covalent geometry : angle 0.60960 (39922) SS BOND : bond 0.00348 ( 45) SS BOND : angle 1.77016 ( 90) hydrogen bonds : bond 0.05561 ( 1170) hydrogen bonds : angle 6.50915 ( 3330) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 287 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 83 MET cc_start: 0.7661 (mtm) cc_final: 0.7456 (mtm) REVERT: D 901 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8810 (tt0) REVERT: D 1017 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: E 900 MET cc_start: 0.7918 (mtm) cc_final: 0.7635 (mtp) REVERT: E 1091 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7788 (mtm-85) REVERT: C 820 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7572 (m-30) outliers start: 56 outliers final: 19 residues processed: 320 average time/residue: 0.6476 time to fit residues: 245.1390 Evaluate side-chains 259 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 901 GLN Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1017 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 1091 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 288 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 339 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 161 optimal weight: 0.4980 chunk 187 optimal weight: 1.9990 chunk 306 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 255 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 35 HIS H 27 GLN H 38 GLN D 422 ASN D 498 GLN D 804 GLN D 935 GLN E 607 GLN E 710 ASN E1010 GLN E1011 GLN E1101 HIS C 239 GLN C 437 ASN C 532 ASN C 580 GLN C 901 GLN C 919 ASN C 957 GLN C1002 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.217584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.198756 restraints weight = 27047.664| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 1.49 r_work: 0.4055 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.4012 rms_B_bonded: 1.75 restraints_weight: 0.2500 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 29388 Z= 0.169 Angle : 0.578 8.687 40012 Z= 0.316 Chirality : 0.045 0.160 4524 Planarity : 0.005 0.060 5173 Dihedral : 4.632 24.230 3947 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.53 % Allowed : 11.50 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.13), residues: 3627 helix: 2.24 (0.19), residues: 693 sheet: 0.93 (0.16), residues: 903 loop : -0.20 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 905 TYR 0.023 0.002 TYR E1067 PHE 0.022 0.002 PHE C 898 TRP 0.012 0.002 TRP E 886 HIS 0.008 0.001 HIS R 35 Details of bonding type rmsd covalent geometry : bond 0.00381 (29343) covalent geometry : angle 0.57221 (39922) SS BOND : bond 0.00347 ( 45) SS BOND : angle 1.82273 ( 90) hydrogen bonds : bond 0.05198 ( 1170) hydrogen bonds : angle 6.04747 ( 3330) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 254 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 ILE cc_start: 0.6850 (OUTLIER) cc_final: 0.6592 (pt) REVERT: H 49 TYR cc_start: 0.8058 (p90) cc_final: 0.7768 (p90) REVERT: D 237 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7656 (mtm110) REVERT: D 429 PHE cc_start: 0.4865 (OUTLIER) cc_final: 0.2491 (p90) REVERT: D 577 ARG cc_start: 0.7756 (ttm170) cc_final: 0.7312 (ttm-80) REVERT: D 613 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: D 804 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7573 (mp-120) REVERT: D 869 MET cc_start: 0.9092 (mtt) cc_final: 0.8470 (mtp) REVERT: D 1017 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: D 1019 ARG cc_start: 0.8210 (ttm110) cc_final: 0.7981 (ttp-110) REVERT: E 900 MET cc_start: 0.7764 (mtm) cc_final: 0.7546 (mtp) REVERT: E 1019 ARG cc_start: 0.8385 (ttp-110) cc_final: 0.8075 (ttm110) REVERT: E 1091 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7802 (mtm-85) outliers start: 81 outliers final: 29 residues processed: 310 average time/residue: 0.6589 time to fit residues: 241.9652 Evaluate side-chains 276 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 613 GLN Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 804 GLN Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 935 GLN Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1017 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 961 THR Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain E residue 1091 ARG Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 88 optimal weight: 5.9990 chunk 291 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 347 optimal weight: 9.9990 chunk 203 optimal weight: 0.9980 chunk 267 optimal weight: 0.9990 chunk 299 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 GLN E1010 GLN C 30 ASN C 239 GLN C 901 GLN C 957 GLN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.216323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.194162 restraints weight = 26887.581| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 1.78 r_work: 0.3995 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 1.90 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 29388 Z= 0.186 Angle : 0.594 10.916 40012 Z= 0.323 Chirality : 0.045 0.173 4524 Planarity : 0.005 0.057 5173 Dihedral : 4.693 24.250 3947 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.38 % Allowed : 12.56 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.13), residues: 3627 helix: 2.08 (0.19), residues: 686 sheet: 0.78 (0.16), residues: 926 loop : -0.26 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 905 TYR 0.023 0.002 TYR C1067 PHE 0.024 0.002 PHE C 898 TRP 0.011 0.002 TRP D 886 HIS 0.006 0.001 HIS R 35 Details of bonding type rmsd covalent geometry : bond 0.00426 (29343) covalent geometry : angle 0.58613 (39922) SS BOND : bond 0.00383 ( 45) SS BOND : angle 2.11558 ( 90) hydrogen bonds : bond 0.05307 ( 1170) hydrogen bonds : angle 5.92908 ( 3330) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 249 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 49 TYR cc_start: 0.8161 (p90) cc_final: 0.7892 (p90) REVERT: D 429 PHE cc_start: 0.5260 (OUTLIER) cc_final: 0.3019 (p90) REVERT: D 613 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7972 (mt0) REVERT: D 1017 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: D 1019 ARG cc_start: 0.8228 (ttm110) cc_final: 0.7986 (ttp-110) REVERT: D 1091 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7356 (mtt-85) REVERT: E 900 MET cc_start: 0.7815 (mtm) cc_final: 0.7578 (mtp) REVERT: E 916 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8495 (tt) REVERT: E 1091 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7693 (mtm-85) REVERT: C 820 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7598 (m-30) outliers start: 76 outliers final: 37 residues processed: 303 average time/residue: 0.6445 time to fit residues: 232.9150 Evaluate side-chains 278 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 613 GLN Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1017 GLU Chi-restraints excluded: chain D residue 1091 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 961 THR Chi-restraints excluded: chain E residue 1091 ARG Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain B residue 23 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 242 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 305 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 222 optimal weight: 0.5980 chunk 360 optimal weight: 9.9990 chunk 77 optimal weight: 0.0670 chunk 266 optimal weight: 0.5980 chunk 285 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN D 901 GLN D 935 GLN E 607 GLN E1010 GLN C 239 GLN C 321 GLN C 957 GLN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.217181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.186256 restraints weight = 26940.862| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.12 r_work: 0.3838 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 29388 Z= 0.139 Angle : 0.548 12.194 40012 Z= 0.295 Chirality : 0.043 0.155 4524 Planarity : 0.004 0.047 5173 Dihedral : 4.456 21.968 3947 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.44 % Allowed : 13.47 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.13), residues: 3627 helix: 2.22 (0.19), residues: 689 sheet: 0.76 (0.16), residues: 923 loop : -0.29 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 905 TYR 0.021 0.001 TYR D1067 PHE 0.019 0.001 PHE E 898 TRP 0.011 0.001 TRP G 107 HIS 0.007 0.001 HIS R 35 Details of bonding type rmsd covalent geometry : bond 0.00317 (29343) covalent geometry : angle 0.53854 (39922) SS BOND : bond 0.00238 ( 45) SS BOND : angle 2.23323 ( 90) hydrogen bonds : bond 0.04672 ( 1170) hydrogen bonds : angle 5.65506 ( 3330) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 251 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 49 TYR cc_start: 0.8264 (p90) cc_final: 0.8018 (p90) REVERT: D 429 PHE cc_start: 0.5237 (OUTLIER) cc_final: 0.3113 (p90) REVERT: D 901 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8770 (tt0) REVERT: D 1017 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: D 1019 ARG cc_start: 0.8228 (ttm110) cc_final: 0.7994 (ttp-110) REVERT: E 900 MET cc_start: 0.7907 (mtm) cc_final: 0.7665 (mtp) REVERT: E 1091 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8124 (mtt90) REVERT: C 820 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7515 (m-30) outliers start: 78 outliers final: 39 residues processed: 311 average time/residue: 0.6391 time to fit residues: 237.0722 Evaluate side-chains 287 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 901 GLN Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1017 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 565 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 961 THR Chi-restraints excluded: chain E residue 1091 ARG Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 23 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 4 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 359 optimal weight: 6.9990 chunk 331 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 chunk 289 optimal weight: 0.8980 chunk 345 optimal weight: 0.2980 chunk 92 optimal weight: 0.9980 chunk 341 optimal weight: 0.2980 chunk 151 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 804 GLN D 901 GLN E 607 GLN E1010 GLN E1101 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.216909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.181049 restraints weight = 26905.647| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.58 r_work: 0.3761 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 29388 Z= 0.143 Angle : 0.561 15.381 40012 Z= 0.301 Chirality : 0.043 0.203 4524 Planarity : 0.004 0.044 5173 Dihedral : 4.418 22.154 3947 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.25 % Allowed : 13.88 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.13), residues: 3627 helix: 2.21 (0.19), residues: 683 sheet: 0.73 (0.16), residues: 932 loop : -0.30 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 905 TYR 0.029 0.001 TYR R 80 PHE 0.023 0.001 PHE C 140 TRP 0.011 0.001 TRP G 107 HIS 0.006 0.001 HIS R 35 Details of bonding type rmsd covalent geometry : bond 0.00328 (29343) covalent geometry : angle 0.54731 (39922) SS BOND : bond 0.00288 ( 45) SS BOND : angle 2.69809 ( 90) hydrogen bonds : bond 0.04654 ( 1170) hydrogen bonds : angle 5.58562 ( 3330) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 247 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 ILE cc_start: 0.7228 (OUTLIER) cc_final: 0.6899 (pt) REVERT: H 49 TYR cc_start: 0.8311 (p90) cc_final: 0.8072 (p90) REVERT: D 346 ARG cc_start: 0.6939 (mmt180) cc_final: 0.6485 (mmp80) REVERT: D 429 PHE cc_start: 0.5366 (OUTLIER) cc_final: 0.3321 (p90) REVERT: D 1017 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: D 1019 ARG cc_start: 0.8244 (ttm110) cc_final: 0.8001 (ttp-110) REVERT: D 1045 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.8003 (mmtm) REVERT: D 1091 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7511 (mtt-85) REVERT: E 900 MET cc_start: 0.7953 (mtm) cc_final: 0.7720 (mtp) REVERT: E 1091 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8067 (mtt90) REVERT: C 820 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7524 (m-30) REVERT: C 916 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8448 (tt) outliers start: 72 outliers final: 38 residues processed: 298 average time/residue: 0.6363 time to fit residues: 226.4649 Evaluate side-chains 279 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 233 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1017 GLU Chi-restraints excluded: chain D residue 1045 LYS Chi-restraints excluded: chain D residue 1091 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 961 THR Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain E residue 1091 ARG Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 23 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 146 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 235 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 359 optimal weight: 0.8980 chunk 342 optimal weight: 0.0870 chunk 171 optimal weight: 2.9990 chunk 341 optimal weight: 0.3980 chunk 203 optimal weight: 0.2980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 804 GLN D 901 GLN E 607 GLN E1010 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 779 GLN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.217123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.171642 restraints weight = 27005.042| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.63 r_work: 0.3554 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 29388 Z= 0.128 Angle : 0.534 11.801 40012 Z= 0.287 Chirality : 0.043 0.183 4524 Planarity : 0.004 0.044 5173 Dihedral : 4.337 21.656 3947 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.97 % Allowed : 14.56 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.13), residues: 3627 helix: 2.24 (0.19), residues: 682 sheet: 0.73 (0.16), residues: 932 loop : -0.28 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 905 TYR 0.021 0.001 TYR D1067 PHE 0.018 0.001 PHE C 898 TRP 0.011 0.001 TRP H 35 HIS 0.006 0.001 HIS R 35 Details of bonding type rmsd covalent geometry : bond 0.00286 (29343) covalent geometry : angle 0.52351 (39922) SS BOND : bond 0.00381 ( 45) SS BOND : angle 2.26528 ( 90) hydrogen bonds : bond 0.04439 ( 1170) hydrogen bonds : angle 5.48493 ( 3330) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 242 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7002 (pt) REVERT: H 49 TYR cc_start: 0.8390 (p90) cc_final: 0.8158 (p90) REVERT: D 346 ARG cc_start: 0.7144 (mmt180) cc_final: 0.6524 (mmp80) REVERT: D 429 PHE cc_start: 0.5440 (OUTLIER) cc_final: 0.3378 (p90) REVERT: D 1017 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: D 1019 ARG cc_start: 0.8285 (ttm110) cc_final: 0.8035 (ttp-110) REVERT: D 1045 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8005 (mmtm) REVERT: D 1091 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7549 (mtt-85) REVERT: E 900 MET cc_start: 0.8042 (mtm) cc_final: 0.7824 (mtp) REVERT: E 916 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8425 (tt) REVERT: E 1091 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8167 (mtt90) REVERT: C 820 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7571 (m-30) REVERT: C 916 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8427 (tt) REVERT: C 1045 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8259 (tptp) REVERT: A 4 MET cc_start: 0.3369 (pmm) cc_final: 0.2756 (ppp) outliers start: 63 outliers final: 35 residues processed: 291 average time/residue: 0.6422 time to fit residues: 222.7250 Evaluate side-chains 279 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1017 GLU Chi-restraints excluded: chain D residue 1045 LYS Chi-restraints excluded: chain D residue 1091 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 565 PHE Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 961 THR Chi-restraints excluded: chain E residue 1091 ARG Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 233 optimal weight: 1.9990 chunk 342 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 201 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 191 optimal weight: 0.8980 chunk 214 optimal weight: 0.3980 chunk 266 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 804 GLN D 913 GLN E 607 GLN E1010 GLN E1101 HIS C 239 GLN C 321 GLN C 779 GLN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.216734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.211666 restraints weight = 26968.967| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 0.30 r_work: 0.4222 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.4181 rms_B_bonded: 1.18 restraints_weight: 0.2500 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 29388 Z= 0.142 Angle : 0.549 15.773 40012 Z= 0.294 Chirality : 0.043 0.206 4524 Planarity : 0.004 0.045 5173 Dihedral : 4.380 22.312 3947 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.94 % Allowed : 15.06 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.13), residues: 3627 helix: 2.22 (0.20), residues: 675 sheet: 0.70 (0.16), residues: 937 loop : -0.27 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 905 TYR 0.022 0.001 TYR R 80 PHE 0.022 0.001 PHE C 92 TRP 0.014 0.001 TRP H 35 HIS 0.006 0.001 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00323 (29343) covalent geometry : angle 0.53788 (39922) SS BOND : bond 0.00369 ( 45) SS BOND : angle 2.37627 ( 90) hydrogen bonds : bond 0.04603 ( 1170) hydrogen bonds : angle 5.47963 ( 3330) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 235 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 ILE cc_start: 0.6470 (OUTLIER) cc_final: 0.6171 (pt) REVERT: H 49 TYR cc_start: 0.8089 (p90) cc_final: 0.7861 (p90) REVERT: D 429 PHE cc_start: 0.5116 (OUTLIER) cc_final: 0.3354 (p90) REVERT: D 1017 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: D 1019 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7921 (ttp-110) REVERT: D 1091 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7399 (mtt-85) REVERT: E 900 MET cc_start: 0.7741 (mtm) cc_final: 0.7492 (mtp) REVERT: E 916 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8461 (tt) REVERT: E 1091 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.8001 (mtt90) REVERT: C 820 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7436 (m-30) REVERT: C 916 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8429 (tt) outliers start: 62 outliers final: 42 residues processed: 284 average time/residue: 0.6329 time to fit residues: 214.9985 Evaluate side-chains 277 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1017 GLU Chi-restraints excluded: chain D residue 1091 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 961 THR Chi-restraints excluded: chain E residue 1091 ARG Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 23 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 80 optimal weight: 8.9990 chunk 302 optimal weight: 2.9990 chunk 318 optimal weight: 0.0970 chunk 179 optimal weight: 0.3980 chunk 194 optimal weight: 3.9990 chunk 362 optimal weight: 30.0000 chunk 214 optimal weight: 0.9980 chunk 285 optimal weight: 3.9990 chunk 56 optimal weight: 0.0040 chunk 134 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN ** R 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 ASN D 613 GLN D 804 GLN E 66 HIS E 607 GLN E1010 GLN C 239 GLN C 321 GLN C 779 GLN C1002 GLN B 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.216864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.182022 restraints weight = 26909.543| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.52 r_work: 0.3774 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 29388 Z= 0.132 Angle : 0.542 14.478 40012 Z= 0.289 Chirality : 0.043 0.192 4524 Planarity : 0.004 0.045 5173 Dihedral : 4.326 21.810 3947 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.81 % Allowed : 15.53 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.13), residues: 3627 helix: 2.33 (0.20), residues: 663 sheet: 0.79 (0.16), residues: 912 loop : -0.28 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 905 TYR 0.021 0.001 TYR D1067 PHE 0.018 0.001 PHE C 898 TRP 0.019 0.001 TRP H 35 HIS 0.006 0.001 HIS R 35 Details of bonding type rmsd covalent geometry : bond 0.00298 (29343) covalent geometry : angle 0.53162 (39922) SS BOND : bond 0.00350 ( 45) SS BOND : angle 2.24010 ( 90) hydrogen bonds : bond 0.04428 ( 1170) hydrogen bonds : angle 5.40796 ( 3330) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 240 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 49 TYR cc_start: 0.8295 (p90) cc_final: 0.8051 (p90) REVERT: D 429 PHE cc_start: 0.5510 (OUTLIER) cc_final: 0.3578 (p90) REVERT: D 869 MET cc_start: 0.9057 (mtt) cc_final: 0.8548 (mtp) REVERT: D 1017 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7874 (tm-30) REVERT: D 1019 ARG cc_start: 0.8253 (ttm110) cc_final: 0.7998 (ttp-110) REVERT: D 1091 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7517 (mtt-85) REVERT: E 900 MET cc_start: 0.7939 (mtm) cc_final: 0.7712 (mtp) REVERT: E 916 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8422 (tt) REVERT: E 1091 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8091 (mtt90) REVERT: C 820 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: C 916 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8445 (tt) outliers start: 58 outliers final: 41 residues processed: 286 average time/residue: 0.6051 time to fit residues: 207.4592 Evaluate side-chains 277 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1017 GLU Chi-restraints excluded: chain D residue 1091 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 961 THR Chi-restraints excluded: chain E residue 1091 ARG Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 23 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 251 optimal weight: 0.9990 chunk 350 optimal weight: 30.0000 chunk 218 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 109 optimal weight: 0.0040 chunk 314 optimal weight: 0.0980 chunk 52 optimal weight: 0.7980 chunk 305 optimal weight: 0.5980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 354 ASN ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN D 542 ASN D 613 GLN D 804 GLN E 607 GLN E1010 GLN C 239 GLN C 321 GLN C 779 GLN C1002 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.217188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.185806 restraints weight = 26810.876| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.18 r_work: 0.3830 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 29388 Z= 0.122 Angle : 0.535 13.772 40012 Z= 0.286 Chirality : 0.043 0.174 4524 Planarity : 0.004 0.045 5173 Dihedral : 4.273 20.953 3947 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.07 % Favored : 97.90 % Rotamer: Outliers : 1.59 % Allowed : 15.84 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.13), residues: 3627 helix: 2.37 (0.20), residues: 664 sheet: 0.81 (0.16), residues: 925 loop : -0.29 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 905 TYR 0.021 0.001 TYR D1067 PHE 0.023 0.001 PHE C 92 TRP 0.023 0.001 TRP H 35 HIS 0.006 0.001 HIS R 35 Details of bonding type rmsd covalent geometry : bond 0.00277 (29343) covalent geometry : angle 0.52506 (39922) SS BOND : bond 0.00291 ( 45) SS BOND : angle 2.22377 ( 90) hydrogen bonds : bond 0.04323 ( 1170) hydrogen bonds : angle 5.35279 ( 3330) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 49 TYR cc_start: 0.8246 (p90) cc_final: 0.8012 (p90) REVERT: D 429 PHE cc_start: 0.5330 (OUTLIER) cc_final: 0.3446 (p90) REVERT: D 869 MET cc_start: 0.9038 (mtt) cc_final: 0.8461 (mtp) REVERT: D 1017 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: D 1019 ARG cc_start: 0.8243 (ttm110) cc_final: 0.7994 (ttp-110) REVERT: D 1091 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7482 (mtt-85) REVERT: E 916 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8369 (tt) REVERT: E 1091 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8113 (mtt90) REVERT: C 820 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: C 916 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8417 (tt) outliers start: 51 outliers final: 39 residues processed: 275 average time/residue: 0.6360 time to fit residues: 209.0424 Evaluate side-chains 274 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1017 GLU Chi-restraints excluded: chain D residue 1091 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain E residue 1091 ARG Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 23 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 295 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 328 optimal weight: 0.5980 chunk 303 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 63 optimal weight: 0.0870 chunk 152 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN E 607 GLN E1101 HIS C 239 GLN C 321 GLN C 779 GLN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.217127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.186082 restraints weight = 27052.139| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.21 r_work: 0.3836 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.189 29388 Z= 0.151 Angle : 0.698 59.200 40012 Z= 0.388 Chirality : 0.044 0.665 4524 Planarity : 0.004 0.045 5173 Dihedral : 4.276 20.995 3947 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.62 % Allowed : 15.66 % Favored : 82.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.13), residues: 3627 helix: 2.33 (0.20), residues: 665 sheet: 0.80 (0.16), residues: 925 loop : -0.29 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 905 TYR 0.021 0.001 TYR D1067 PHE 0.022 0.001 PHE C 92 TRP 0.019 0.001 TRP H 35 HIS 0.006 0.001 HIS R 35 Details of bonding type rmsd covalent geometry : bond 0.00327 (29343) covalent geometry : angle 0.68096 (39922) SS BOND : bond 0.00753 ( 45) SS BOND : angle 3.29085 ( 90) hydrogen bonds : bond 0.04358 ( 1170) hydrogen bonds : angle 5.35461 ( 3330) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10695.88 seconds wall clock time: 183 minutes 20.60 seconds (11000.60 seconds total)