Starting phenix.real_space_refine on Thu May 29 16:12:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q5y_18180/05_2025/8q5y_18180.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q5y_18180/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8q5y_18180/05_2025/8q5y_18180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q5y_18180/05_2025/8q5y_18180.map" model { file = "/net/cci-nas-00/data/ceres_data/8q5y_18180/05_2025/8q5y_18180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q5y_18180/05_2025/8q5y_18180.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.63, per 1000 atoms: 0.54 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: 6.11 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 4.86 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: 15.82 Time building geometry restraints manager: 7.34 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: 8.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 1.220 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 68.350 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 92.390 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.121 0.004 TRP E 886 HIS 0.013 0.003 HIS D 655 PHE 0.101 0.003 PHE C 906 TYR 0.059 0.003 TYR L 86 ARG 0.021 0.001 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.18836 ( 1170) hydrogen bonds : angle 8.62053 ( 3330) SS BOND : bond 0.00567 ( 45) SS BOND : angle 2.79241 ( 90) covalent geometry : bond 0.00631 (29343) covalent geometry : angle 1.06425 (39922) *********************** 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 : 3.170 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: 1.3210 time to fit residues: 744.4236 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 : 2.924 ------------------------------------------------------------------------------- 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 308 optimal weight: 0.7980 chunk 276 optimal weight: 0.9990 chunk 153 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 chunk 110 optimal weight: 0.0010 chunk 173 optimal weight: 0.0770 chunk 212 optimal weight: 0.9980 chunk 331 optimal weight: 0.9990 overall best weight: 0.4744 ------------------------------------------------------------------------------- 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 196 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 E 354 ASN E 607 GLN 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 935 GLN C 954 GLN C1010 GLN ** B 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.221614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.215773 restraints weight = 27340.341| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 0.34 r_work: 0.4266 rms_B_bonded: 0.72 restraints_weight: 0.5000 r_work: 0.4225 rms_B_bonded: 1.27 restraints_weight: 0.2500 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 29388 Z= 0.146 Angle : 0.578 9.417 40012 Z= 0.317 Chirality : 0.045 0.193 4524 Planarity : 0.005 0.073 5173 Dihedral : 4.575 33.181 3953 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.59 % Allowed : 9.62 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.13), residues: 3627 helix: 2.76 (0.18), residues: 699 sheet: 1.09 (0.16), residues: 906 loop : -0.07 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 886 HIS 0.005 0.001 HIS R 35 PHE 0.023 0.002 PHE D 906 TYR 0.034 0.002 TYR C 200 ARG 0.009 0.001 ARG D 454 Details of bonding type rmsd hydrogen bonds : bond 0.05196 ( 1170) hydrogen bonds : angle 6.46998 ( 3330) SS BOND : bond 0.00283 ( 45) SS BOND : angle 1.84789 ( 90) covalent geometry : bond 0.00324 (29343) covalent geometry : angle 0.57206 (39922) *********************** 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 353 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 302 time to evaluate : 3.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 901 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8715 (tt0) REVERT: D 1017 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: E 900 MET cc_start: 0.7714 (mtm) cc_final: 0.7384 (mtp) REVERT: E 1045 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7792 (mmtm) REVERT: C 1010 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7872 (tm130) outliers start: 51 outliers final: 15 residues processed: 333 average time/residue: 1.2922 time to fit residues: 511.3705 Evaluate side-chains 272 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 254 time to evaluate : 3.063 ------------------------------------------------------------------------------- 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 309 GLU 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 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 546 LEU Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1010 GLN 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 196 optimal weight: 0.9990 chunk 334 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 211 optimal weight: 0.0570 chunk 132 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- 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 G 59 HIS H 27 GLN D 388 ASN D 422 ASN D 498 GLN D 542 ASN D 804 GLN D 935 GLN D1002 GLN E 607 GLN E1010 GLN E1011 GLN E1101 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 580 GLN C 901 GLN C 926 GLN 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 = 0.4368 r_free = 0.4368 target = 0.219299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.213545 restraints weight = 26891.059| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 0.33 r_work: 0.4240 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.4198 rms_B_bonded: 1.28 restraints_weight: 0.2500 r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.2068 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= 0.150 Angle : 0.565 10.467 40012 Z= 0.307 Chirality : 0.045 0.160 4524 Planarity : 0.004 0.057 5173 Dihedral : 4.486 23.652 3947 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.25 % Allowed : 11.75 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.13), residues: 3627 helix: 2.46 (0.19), residues: 688 sheet: 0.92 (0.16), residues: 911 loop : -0.17 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 886 HIS 0.008 0.001 HIS R 35 PHE 0.019 0.002 PHE C 898 TYR 0.023 0.002 TYR C 200 ARG 0.007 0.001 ARG C1014 Details of bonding type rmsd hydrogen bonds : bond 0.05029 ( 1170) hydrogen bonds : angle 6.02683 ( 3330) SS BOND : bond 0.00293 ( 45) SS BOND : angle 1.78333 ( 90) covalent geometry : bond 0.00340 (29343) covalent geometry : angle 0.55880 (39922) *********************** 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 338 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 266 time to evaluate : 3.022 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: 0.6605 (OUTLIER) cc_final: 0.6336 (pt) REVERT: D 429 PHE cc_start: 0.4443 (OUTLIER) cc_final: 0.2155 (p90) REVERT: D 577 ARG cc_start: 0.7672 (ttm170) cc_final: 0.7282 (ttm-80) REVERT: D 804 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7352 (mp-120) REVERT: D 1017 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: D 1091 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6931 (mtp-110) REVERT: E 900 MET cc_start: 0.7706 (mtm) cc_final: 0.7476 (mtp) REVERT: E 1045 LYS cc_start: 0.8090 (mmtm) cc_final: 0.7886 (mmtm) REVERT: E 1091 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7774 (mtm-85) outliers start: 72 outliers final: 27 residues processed: 316 average time/residue: 1.2808 time to fit residues: 480.5881 Evaluate side-chains 284 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 251 time to evaluate : 2.935 ------------------------------------------------------------------------------- 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 64 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 591 SER 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 D residue 1091 ARG Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 1010 GLN 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 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 1122 VAL 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 224 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 317 optimal weight: 0.6980 chunk 341 optimal weight: 0.5980 chunk 144 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 302 optimal weight: 3.9990 chunk 354 optimal weight: 20.0000 chunk 268 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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** H 38 GLN ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN D 935 GLN E 607 GLN E 935 GLN E1010 GLN E1101 HIS C 30 ASN C 239 GLN C 532 ASN C 580 GLN C 901 GLN C 919 ASN C 957 GLN C1002 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.214589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.188407 restraints weight = 26881.314| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.16 r_work: 0.3915 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3867 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 29388 Z= 0.287 Angle : 0.701 10.936 40012 Z= 0.384 Chirality : 0.050 0.254 4524 Planarity : 0.006 0.098 5173 Dihedral : 5.126 26.694 3947 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.69 % Allowed : 12.53 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.13), residues: 3627 helix: 1.57 (0.19), residues: 686 sheet: 0.70 (0.16), residues: 917 loop : -0.31 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 886 HIS 0.010 0.002 HIS D1048 PHE 0.034 0.003 PHE C 898 TYR 0.026 0.002 TYR E1067 ARG 0.015 0.001 ARG E 905 Details of bonding type rmsd hydrogen bonds : bond 0.06244 ( 1170) hydrogen bonds : angle 6.15110 ( 3330) SS BOND : bond 0.00476 ( 45) SS BOND : angle 2.28749 ( 90) covalent geometry : bond 0.00666 (29343) covalent geometry : angle 0.69338 (39922) *********************** 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 339 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 253 time to evaluate : 3.138 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 48 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6780 (pt) REVERT: D 429 PHE cc_start: 0.5606 (OUTLIER) cc_final: 0.3370 (p90) REVERT: D 858 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8067 (mt) REVERT: D 901 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8779 (tt0) REVERT: D 1017 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: D 1091 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7116 (mtp-110) REVERT: E 916 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8415 (tt) REVERT: E 1091 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7797 (mtm-85) REVERT: C 820 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7723 (m-30) outliers start: 86 outliers final: 38 residues processed: 316 average time/residue: 1.1981 time to fit residues: 455.5650 Evaluate side-chains 277 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 230 time to evaluate : 3.231 ------------------------------------------------------------------------------- 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 105 ASP Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain D residue 127 VAL 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 616 ASN Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 858 LEU 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 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 386 LYS Chi-restraints excluded: chain E residue 445 VAL 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 C residue 51 THR Chi-restraints excluded: chain C residue 429 PHE 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 1122 VAL 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 234 optimal weight: 0.5980 chunk 284 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 306 optimal weight: 0.9980 chunk 227 optimal weight: 0.5980 chunk 275 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 203 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 ASN D 498 GLN D 804 GLN D 935 GLN E 607 GLN E 935 GLN E1010 GLN C 239 GLN C 321 GLN C 957 GLN C1002 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.215905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.179490 restraints weight = 26863.616| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.63 r_work: 0.3736 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 29388 Z= 0.168 Angle : 0.579 12.903 40012 Z= 0.315 Chirality : 0.044 0.205 4524 Planarity : 0.005 0.048 5173 Dihedral : 4.723 23.718 3947 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.41 % Allowed : 13.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.13), residues: 3627 helix: 1.98 (0.19), residues: 683 sheet: 0.67 (0.16), residues: 952 loop : -0.35 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 107 HIS 0.007 0.001 HIS D 655 PHE 0.023 0.002 PHE E 898 TYR 0.022 0.002 TYR C1067 ARG 0.008 0.000 ARG E 905 Details of bonding type rmsd hydrogen bonds : bond 0.05061 ( 1170) hydrogen bonds : angle 5.81254 ( 3330) SS BOND : bond 0.00383 ( 45) SS BOND : angle 2.45202 ( 90) covalent geometry : bond 0.00385 (29343) covalent geometry : angle 0.56791 (39922) *********************** 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 322 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 245 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 429 PHE cc_start: 0.5488 (OUTLIER) cc_final: 0.3564 (p90) REVERT: D 858 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8066 (mt) REVERT: D 1017 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: D 1091 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7247 (mtp-110) REVERT: E 1091 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8002 (mtt-85) REVERT: C 820 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: C 1045 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8216 (tptp) outliers start: 77 outliers final: 36 residues processed: 298 average time/residue: 1.2224 time to fit residues: 436.8608 Evaluate side-chains 278 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 2.965 ------------------------------------------------------------------------------- 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 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 786 LYS Chi-restraints excluded: chain D residue 858 LEU 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 386 LYS Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 565 PHE 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 317 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR 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 1045 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 66 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 275 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 66 HIS ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 913 GLN D1135 ASN E 66 HIS E 607 GLN E1010 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.213099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.199603 restraints weight = 26774.361| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 0.98 r_work: 0.4087 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.4037 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.157 29388 Z= 0.298 Angle : 0.730 19.136 40012 Z= 0.395 Chirality : 0.050 0.207 4524 Planarity : 0.006 0.098 5173 Dihedral : 5.181 25.915 3947 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.72 % Allowed : 13.94 % Favored : 83.34 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.13), residues: 3627 helix: 1.33 (0.19), residues: 691 sheet: 0.55 (0.16), residues: 945 loop : -0.44 (0.13), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 886 HIS 0.012 0.002 HIS D 655 PHE 0.035 0.003 PHE E 898 TYR 0.030 0.002 TYR R 80 ARG 0.020 0.001 ARG E 905 Details of bonding type rmsd hydrogen bonds : bond 0.06192 ( 1170) hydrogen bonds : angle 6.03326 ( 3330) SS BOND : bond 0.00508 ( 45) SS BOND : angle 3.26030 ( 90) covalent geometry : bond 0.00694 (29343) covalent geometry : angle 0.71475 (39922) *********************** 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 338 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 251 time to evaluate : 3.358 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: 0.6864 (OUTLIER) cc_final: 0.6593 (pt) REVERT: D 429 PHE cc_start: 0.5768 (OUTLIER) cc_final: 0.4010 (p90) REVERT: D 858 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.7923 (mt) REVERT: D 983 ARG cc_start: 0.7018 (mtm180) cc_final: 0.6805 (ptp90) REVERT: D 1017 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7798 (tm-30) REVERT: D 1091 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7194 (mtp-110) REVERT: E 444 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7138 (ptpt) REVERT: E 1091 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8069 (mtt-85) REVERT: E 1113 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7825 (mt0) REVERT: C 820 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: C 1045 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8280 (tptp) outliers start: 87 outliers final: 49 residues processed: 320 average time/residue: 1.2103 time to fit residues: 468.6623 Evaluate side-chains 293 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 234 time to evaluate : 3.086 ------------------------------------------------------------------------------- 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 64 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 127 VAL 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 326 ILE Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 498 GLN 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 785 VAL Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 858 LEU 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 D residue 1096 VAL Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 445 VAL 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 1076 THR Chi-restraints excluded: chain E residue 1086 LYS Chi-restraints excluded: chain E residue 1091 ARG Chi-restraints excluded: chain E residue 1113 GLN 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 429 PHE Chi-restraints excluded: chain C residue 553 THR 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 1045 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 63 optimal weight: 0.0770 chunk 244 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 333 optimal weight: 0.0070 chunk 296 optimal weight: 0.9980 chunk 235 optimal weight: 0.0870 chunk 156 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 239 optimal weight: 0.5980 chunk 260 optimal weight: 1.9990 overall best weight: 0.3534 ------------------------------------------------------------------------------- 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 354 ASN ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 ASN D 450 ASN E 607 GLN E1010 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 779 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 = 0.4339 r_free = 0.4339 target = 0.216316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.181847 restraints weight = 26893.914| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.47 r_work: 0.3770 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 29388 Z= 0.124 Angle : 0.547 12.524 40012 Z= 0.294 Chirality : 0.043 0.304 4524 Planarity : 0.004 0.045 5173 Dihedral : 4.506 22.144 3947 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.88 % Allowed : 15.03 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.13), residues: 3627 helix: 1.93 (0.19), residues: 699 sheet: 0.65 (0.16), residues: 958 loop : -0.36 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 35 HIS 0.007 0.001 HIS R 35 PHE 0.018 0.001 PHE E 759 TYR 0.022 0.001 TYR D1067 ARG 0.004 0.000 ARG C1014 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 1170) hydrogen bonds : angle 5.56291 ( 3330) SS BOND : bond 0.00434 ( 45) SS BOND : angle 2.41308 ( 90) covalent geometry : bond 0.00281 (29343) covalent geometry : angle 0.53581 (39922) *********************** 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 319 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 259 time to evaluate : 3.134 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: D 858 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8012 (mt) REVERT: D 869 MET cc_start: 0.9045 (mtt) cc_final: 0.8657 (mtp) REVERT: D 983 ARG cc_start: 0.7075 (mtm180) cc_final: 0.6862 (ptp90) REVERT: D 1017 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: D 1045 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7863 (mmtt) REVERT: D 1091 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7179 (mtp-110) REVERT: E 916 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8303 (tt) REVERT: E 1045 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7900 (mmtm) REVERT: E 1091 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7839 (mtt-85) REVERT: C 820 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7492 (m-30) REVERT: C 878 LEU cc_start: 0.8802 (tp) cc_final: 0.8566 (mt) outliers start: 60 outliers final: 33 residues processed: 303 average time/residue: 1.2389 time to fit residues: 449.4167 Evaluate side-chains 284 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 244 time to evaluate : 3.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 858 LEU 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 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 445 VAL Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 791 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 130 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 553 THR 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 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 A residue 4 MET Chi-restraints excluded: chain B residue 23 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 137 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 286 optimal weight: 0.8980 chunk 250 optimal weight: 7.9990 chunk 255 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 228 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 314 GLN ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN E 607 GLN E1010 GLN E1101 HIS C 239 GLN C 321 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C 957 GLN C1002 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.213604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.176549 restraints weight = 26769.372| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.67 r_work: 0.3703 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.161 29388 Z= 0.244 Angle : 0.674 19.377 40012 Z= 0.362 Chirality : 0.047 0.297 4524 Planarity : 0.005 0.083 5173 Dihedral : 4.927 25.123 3947 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.16 % Allowed : 15.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.13), residues: 3627 helix: 1.53 (0.19), residues: 680 sheet: 0.58 (0.16), residues: 961 loop : -0.43 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 35 HIS 0.010 0.002 HIS D 655 PHE 0.029 0.002 PHE E 898 TYR 0.024 0.002 TYR E1067 ARG 0.014 0.001 ARG E 905 Details of bonding type rmsd hydrogen bonds : bond 0.05695 ( 1170) hydrogen bonds : angle 5.81476 ( 3330) SS BOND : bond 0.00552 ( 45) SS BOND : angle 3.04025 ( 90) covalent geometry : bond 0.00567 (29343) covalent geometry : angle 0.65921 (39922) *********************** 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 315 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 246 time to evaluate : 3.457 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: D 429 PHE cc_start: 0.6035 (OUTLIER) cc_final: 0.4134 (p90) REVERT: D 858 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8062 (mt) REVERT: D 869 MET cc_start: 0.9074 (mtt) cc_final: 0.8544 (mtp) REVERT: D 983 ARG cc_start: 0.7152 (mtm180) cc_final: 0.6902 (ptp90) REVERT: D 1017 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: D 1045 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7912 (mmtt) REVERT: D 1091 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7305 (mtp-110) REVERT: E 1091 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8112 (mtt-85) REVERT: C 203 ILE cc_start: 0.8312 (tp) cc_final: 0.8110 (tp) REVERT: C 820 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7724 (m-30) REVERT: C 878 LEU cc_start: 0.8795 (tp) cc_final: 0.8543 (mt) outliers start: 69 outliers final: 44 residues processed: 293 average time/residue: 1.2743 time to fit residues: 449.7616 Evaluate side-chains 288 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 237 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 127 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 309 GLU Chi-restraints excluded: chain D residue 429 PHE Chi-restraints excluded: chain D residue 515 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 786 LYS Chi-restraints excluded: chain D residue 858 LEU 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 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 285 ILE Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 614 ASP Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 791 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 553 THR 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 811 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1130 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 280 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 257 optimal weight: 0.5980 chunk 341 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 330 optimal weight: 0.6980 chunk 207 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 339 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 52 GLN D 314 GLN ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 GLN E1010 GLN C 239 GLN C 321 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.214437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.208236 restraints weight = 26716.932| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 0.34 r_work: 0.4184 rms_B_bonded: 0.74 restraints_weight: 0.5000 r_work: 0.4141 rms_B_bonded: 1.29 restraints_weight: 0.2500 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 29388 Z= 0.165 Angle : 0.594 16.869 40012 Z= 0.318 Chirality : 0.044 0.303 4524 Planarity : 0.004 0.048 5173 Dihedral : 4.679 24.579 3947 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.97 % Allowed : 15.28 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.13), residues: 3627 helix: 1.85 (0.20), residues: 675 sheet: 0.63 (0.16), residues: 954 loop : -0.41 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 35 HIS 0.007 0.001 HIS D 655 PHE 0.022 0.001 PHE E 898 TYR 0.023 0.002 TYR D1067 ARG 0.007 0.000 ARG E 905 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 1170) hydrogen bonds : angle 5.59990 ( 3330) SS BOND : bond 0.00485 ( 45) SS BOND : angle 2.67607 ( 90) covalent geometry : bond 0.00382 (29343) covalent geometry : angle 0.58049 (39922) *********************** 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 310 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 247 time to evaluate : 3.322 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: D 429 PHE cc_start: 0.5642 (OUTLIER) cc_final: 0.3870 (p90) REVERT: D 858 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7940 (mt) REVERT: D 869 MET cc_start: 0.9039 (mtt) cc_final: 0.8521 (mtp) REVERT: D 1017 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: D 1045 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7800 (mmtt) REVERT: D 1091 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7103 (mtp-110) REVERT: E 916 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8434 (tt) REVERT: E 1091 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7781 (mtt-85) REVERT: C 820 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: C 878 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8530 (mt) outliers start: 63 outliers final: 45 residues processed: 291 average time/residue: 1.1497 time to fit residues: 403.0737 Evaluate side-chains 291 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 237 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 127 VAL 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 515 PHE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 858 LEU 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 1045 LYS Chi-restraints excluded: chain D residue 1091 ARG Chi-restraints excluded: chain E residue 29 THR 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 614 ASP Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 961 THR Chi-restraints excluded: chain E residue 990 GLU Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain E residue 1086 LYS 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 525 CYS Chi-restraints excluded: chain C residue 553 THR 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 1126 CYS Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain A residue 4 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 15 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 216 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 chunk 45 optimal weight: 0.0470 chunk 67 optimal weight: 5.9990 chunk 210 optimal weight: 0.0020 chunk 325 optimal weight: 0.8980 chunk 226 optimal weight: 0.9990 overall best weight: 0.5086 ------------------------------------------------------------------------------- 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** E 607 GLN E1010 GLN C 239 GLN C 321 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C1002 GLN B 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.214996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.179558 restraints weight = 26815.718| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.54 r_work: 0.3740 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 29388 Z= 0.141 Angle : 0.577 14.892 40012 Z= 0.308 Chirality : 0.044 0.305 4524 Planarity : 0.004 0.045 5173 Dihedral : 4.587 24.465 3947 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.97 % Allowed : 15.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.13), residues: 3627 helix: 1.94 (0.20), residues: 681 sheet: 0.64 (0.16), residues: 963 loop : -0.39 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 35 HIS 0.007 0.001 HIS R 35 PHE 0.022 0.001 PHE C 92 TYR 0.023 0.001 TYR D1067 ARG 0.005 0.000 ARG E 905 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 1170) hydrogen bonds : angle 5.52162 ( 3330) SS BOND : bond 0.00551 ( 45) SS BOND : angle 2.54650 ( 90) covalent geometry : bond 0.00326 (29343) covalent geometry : angle 0.56496 (39922) ********************** 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 313 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 250 time to evaluate : 3.000 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: D 858 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8065 (mt) REVERT: D 869 MET cc_start: 0.9063 (mtt) cc_final: 0.8510 (mtp) REVERT: D 1017 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: D 1045 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7867 (mmtt) REVERT: D 1091 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7223 (mtp-110) REVERT: E 916 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8383 (tt) REVERT: E 1045 LYS cc_start: 0.8266 (mmtm) cc_final: 0.8001 (mmtm) REVERT: E 1091 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7890 (mtt-85) REVERT: C 820 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: C 878 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8553 (mt) outliers start: 63 outliers final: 44 residues processed: 292 average time/residue: 1.2217 time to fit residues: 432.4295 Evaluate side-chains 292 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 240 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 127 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 309 GLU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 858 LEU 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 D residue 1045 LYS Chi-restraints excluded: chain D residue 1091 ARG Chi-restraints excluded: chain E residue 29 THR 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 445 VAL Chi-restraints excluded: chain E residue 614 ASP Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 791 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 525 CYS Chi-restraints excluded: chain C residue 553 THR 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 1126 CYS Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain A residue 4 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 209 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 345 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 218 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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** E 607 GLN E1010 GLN E1101 HIS C 239 GLN C 321 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C 957 GLN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.212565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.207407 restraints weight = 26651.902| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 0.30 r_work: 0.4178 rms_B_bonded: 0.65 restraints_weight: 0.5000 r_work: 0.4136 rms_B_bonded: 1.17 restraints_weight: 0.2500 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 29388 Z= 0.273 Angle : 0.714 18.086 40012 Z= 0.385 Chirality : 0.049 0.316 4524 Planarity : 0.006 0.088 5173 Dihedral : 5.105 26.458 3947 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 2.06 % Allowed : 15.41 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.13), residues: 3627 helix: 1.38 (0.19), residues: 672 sheet: 0.60 (0.16), residues: 949 loop : -0.51 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP H 35 HIS 0.010 0.002 HIS D 655 PHE 0.032 0.002 PHE E 898 TYR 0.027 0.002 TYR E1067 ARG 0.016 0.001 ARG E 905 Details of bonding type rmsd hydrogen bonds : bond 0.06015 ( 1170) hydrogen bonds : angle 5.84977 ( 3330) SS BOND : bond 0.00603 ( 45) SS BOND : angle 3.12087 ( 90) covalent geometry : bond 0.00635 (29343) covalent geometry : angle 0.69892 (39922) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19274.23 seconds wall clock time: 333 minutes 46.40 seconds (20026.40 seconds total)