Starting phenix.real_space_refine on Thu Jun 19 23:43:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tld_25988/06_2025/7tld_25988.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tld_25988/06_2025/7tld_25988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tld_25988/06_2025/7tld_25988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tld_25988/06_2025/7tld_25988.map" model { file = "/net/cci-nas-00/data/ceres_data/7tld_25988/06_2025/7tld_25988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tld_25988/06_2025/7tld_25988.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 14586 2.51 5 N 3786 2.21 5 O 4335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22812 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 52, 'TRANS': 919} Chain breaks: 11 Chain: "B" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 52, 'TRANS': 919} Chain breaks: 11 Chain: "C" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 52, 'TRANS': 919} Chain breaks: 11 Time building chain proxies: 14.24, per 1000 atoms: 0.62 Number of scatterers: 22812 At special positions: 0 Unit cell: (139.656, 126.96, 170.338, 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 105 16.00 O 4335 8.00 N 3786 7.00 C 14586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS C 383 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.00 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 985 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=2.00 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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: 5.88 Conformation dependent library (CDL) restraints added in 3.0 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 47 sheets defined 27.5% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.095A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.077A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.455A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.818A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.874A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.771A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.737A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.556A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.539A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.837A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.652A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.770A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.298A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.985A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.004A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.666A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.841A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.752A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.539A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.504A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.535A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.265A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.992A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.153A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.075A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.715A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.766A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.626A 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 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.506A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.756A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.508A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.447A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.069A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.365A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.206A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.809A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.695A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.321A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.099A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.099A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.738A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.557A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.591A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.165A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.355A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.808A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.564A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.631A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.691A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.205A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.296A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.384A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.949A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.890A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.430A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.530A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.751A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.489A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.497A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.465A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 52 removed outlier: 7.280A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.175A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.034A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.047A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.047A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.891A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.500A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.621A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.215A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.551A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1031 hydrogen bonds defined for protein. 2826 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: 11.24 Time building geometry restraints manager: 7.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5963 1.33 - 1.46: 4425 1.46 - 1.58: 12808 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 23325 Sorted by residual: bond pdb=" CA HIS A1083 " pdb=" C HIS A1083 " ideal model delta sigma weight residual 1.519 1.543 -0.024 5.30e-03 3.56e+04 2.07e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.68e+01 bond pdb=" CZ ARG A 905 " pdb=" NH2 ARG A 905 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.63e+00 bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.538 -0.021 6.70e-03 2.23e+04 9.59e+00 bond pdb=" CZ ARG B1039 " pdb=" NH2 ARG B1039 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.57e+00 ... (remaining 23320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 24513 2.15 - 4.31: 6673 4.31 - 6.46: 532 6.46 - 8.61: 21 8.61 - 10.76: 1 Bond angle restraints: 31740 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 119.23 -8.53 1.22e+00 6.72e-01 4.89e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 118.44 -7.74 1.22e+00 6.72e-01 4.03e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 117.94 -7.24 1.22e+00 6.72e-01 3.52e+01 angle pdb=" N PRO C 862 " pdb=" CA PRO C 862 " pdb=" CB PRO C 862 " ideal model delta sigma weight residual 103.22 106.14 -2.92 5.20e-01 3.70e+00 3.16e+01 angle pdb=" CA HIS B 207 " pdb=" CB HIS B 207 " pdb=" CG HIS B 207 " ideal model delta sigma weight residual 113.80 119.42 -5.62 1.00e+00 1.00e+00 3.15e+01 ... (remaining 31735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12953 17.93 - 35.86: 771 35.86 - 53.79: 136 53.79 - 71.73: 50 71.73 - 89.66: 31 Dihedral angle restraints: 13941 sinusoidal: 5451 harmonic: 8490 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -162.94 76.94 1 1.00e+01 1.00e-02 7.43e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -150.22 64.22 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 152.19 -59.19 1 1.00e+01 1.00e-02 4.68e+01 ... (remaining 13938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2099 0.076 - 0.152: 1223 0.152 - 0.228: 256 0.228 - 0.305: 45 0.305 - 0.381: 10 Chirality restraints: 3633 Sorted by residual: chirality pdb=" CA PRO C 986 " pdb=" N PRO C 986 " pdb=" C PRO C 986 " pdb=" CB PRO C 986 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA PRO A 986 " pdb=" N PRO A 986 " pdb=" C PRO A 986 " pdb=" CB PRO A 986 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA PRO B 986 " pdb=" N PRO B 986 " pdb=" C PRO B 986 " pdb=" CB PRO B 986 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 3630 not shown) Planarity restraints: 4107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 279 " -0.149 2.00e-02 2.50e+03 8.14e-02 1.33e+02 pdb=" CG TYR B 279 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR B 279 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR B 279 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR B 279 " 0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR B 279 " 0.041 2.00e-02 2.50e+03 pdb=" CZ TYR B 279 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 279 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 269 " 0.144 2.00e-02 2.50e+03 7.42e-02 1.10e+02 pdb=" CG TYR C 269 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR C 269 " -0.071 2.00e-02 2.50e+03 pdb=" CD2 TYR C 269 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR C 269 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR C 269 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR C 269 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 269 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 279 " 0.121 2.00e-02 2.50e+03 6.74e-02 9.07e+01 pdb=" CG TYR A 279 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 279 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR A 279 " -0.057 2.00e-02 2.50e+03 pdb=" CE1 TYR A 279 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR A 279 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR A 279 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 279 " 0.108 2.00e-02 2.50e+03 ... (remaining 4104 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 11105 3.00 - 3.47: 21932 3.47 - 3.95: 38444 3.95 - 4.42: 43176 4.42 - 4.90: 73564 Nonbonded interactions: 188221 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.524 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.527 3.040 nonbonded pdb=" OG SER B 591 " pdb=" OE1 GLU B 619 " model vdw 2.529 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.535 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.554 3.040 ... (remaining 188216 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 58.540 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.110 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:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4541 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 : 0.013 0.045 23364 Z= 0.743 Angle : 1.804 10.763 31818 Z= 1.230 Chirality : 0.093 0.381 3633 Planarity : 0.014 0.203 4107 Dihedral : 13.313 89.656 8340 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 0.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.24 % Favored : 94.59 % Rotamer: Outliers : 0.94 % Allowed : 2.42 % Favored : 96.65 % 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: -1.25 (0.14), residues: 2844 helix: -1.11 (0.16), residues: 669 sheet: -0.11 (0.20), residues: 588 loop : -0.93 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.023 TRP B 104 HIS 0.011 0.003 HIS C 207 PHE 0.088 0.012 PHE B 718 TYR 0.149 0.020 TYR B 279 ARG 0.009 0.001 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.14939 ( 1021) hydrogen bonds : angle 8.44314 ( 2826) SS BOND : bond 0.01542 ( 39) SS BOND : angle 2.26566 ( 78) covalent geometry : bond 0.01257 (23325) covalent geometry : angle 1.80281 (31740) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 372 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.3665 (pt0) cc_final: 0.3266 (mt-10) REVERT: A 305 SER cc_start: 0.7088 (t) cc_final: 0.6679 (t) REVERT: A 307 THR cc_start: 0.6899 (m) cc_final: 0.6502 (p) REVERT: A 309 GLU cc_start: 0.5304 (mp0) cc_final: 0.5101 (pt0) REVERT: A 314 GLN cc_start: 0.5945 (tt0) cc_final: 0.5222 (tp40) REVERT: A 558 LYS cc_start: 0.6950 (tttt) cc_final: 0.6413 (mttp) REVERT: A 584 ILE cc_start: 0.6067 (mm) cc_final: 0.5864 (mp) REVERT: A 661 GLU cc_start: 0.6597 (mt-10) cc_final: 0.5644 (mm-30) REVERT: A 702 GLU cc_start: 0.7202 (tt0) cc_final: 0.6373 (mm-30) REVERT: A 704 SER cc_start: 0.7259 (p) cc_final: 0.7022 (t) REVERT: A 779 GLN cc_start: 0.5003 (tp40) cc_final: 0.4460 (tp40) REVERT: A 780 GLU cc_start: 0.5789 (mt-10) cc_final: 0.4920 (mm-30) REVERT: A 814 LYS cc_start: 0.5978 (mttp) cc_final: 0.5697 (mtpm) REVERT: A 854 LYS cc_start: 0.2788 (mttp) cc_final: 0.2310 (ptmt) REVERT: A 985 CYS cc_start: 0.5578 (p) cc_final: 0.4310 (p) REVERT: A 988 GLU cc_start: 0.4866 (tp30) cc_final: 0.4457 (pm20) REVERT: A 1050 MET cc_start: 0.7242 (ptp) cc_final: 0.7025 (ptm) REVERT: A 1107 ARG cc_start: 0.6447 (mtm180) cc_final: 0.5589 (mtt180) REVERT: B 237 ARG cc_start: 0.5234 (mtt90) cc_final: 0.4884 (mtp-110) REVERT: B 269 TYR cc_start: 0.6625 (m-80) cc_final: 0.6302 (m-80) REVERT: B 271 GLN cc_start: 0.4384 (mt0) cc_final: 0.4055 (mp10) REVERT: B 278 LYS cc_start: 0.3679 (tttt) cc_final: 0.3451 (tttt) REVERT: B 314 GLN cc_start: 0.6883 (tt0) cc_final: 0.6352 (tt0) REVERT: B 317 ASN cc_start: 0.7021 (m-40) cc_final: 0.6544 (m110) REVERT: B 319 ARG cc_start: 0.6135 (mtm180) cc_final: 0.5877 (mtt-85) REVERT: B 355 ARG cc_start: 0.6221 (ttt90) cc_final: 0.6018 (ttm-80) REVERT: B 389 ASP cc_start: 0.6291 (t0) cc_final: 0.5852 (m-30) REVERT: B 554 GLU cc_start: 0.6194 (mt-10) cc_final: 0.5860 (mm-30) REVERT: B 569 ILE cc_start: 0.5819 (mm) cc_final: 0.5590 (tt) REVERT: B 646 ARG cc_start: 0.6353 (ttm170) cc_final: 0.5287 (tpt170) REVERT: B 661 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6631 (mt-10) REVERT: B 697 MET cc_start: 0.6917 (ptm) cc_final: 0.6571 (ptp) REVERT: B 702 GLU cc_start: 0.7074 (tt0) cc_final: 0.6842 (tt0) REVERT: B 735 SER cc_start: 0.6481 (t) cc_final: 0.5727 (p) REVERT: B 750 SER cc_start: 0.5494 (t) cc_final: 0.5088 (m) REVERT: B 790 LYS cc_start: 0.6958 (pttt) cc_final: 0.6096 (ptmm) REVERT: B 814 LYS cc_start: 0.6289 (mttt) cc_final: 0.5238 (mmmt) REVERT: B 912 THR cc_start: 0.6574 (m) cc_final: 0.6149 (p) REVERT: B 947 LYS cc_start: 0.6290 (mttt) cc_final: 0.5962 (mtpt) REVERT: B 957 GLN cc_start: 0.4909 (tp-100) cc_final: 0.4551 (tt0) REVERT: B 988 GLU cc_start: 0.4714 (tp30) cc_final: 0.3986 (mp0) REVERT: B 990 GLU cc_start: 0.4664 (mt-10) cc_final: 0.4310 (tt0) REVERT: B 1010 GLN cc_start: 0.4676 (mm-40) cc_final: 0.3762 (pt0) REVERT: B 1045 LYS cc_start: 0.6746 (ttpp) cc_final: 0.5969 (mptp) REVERT: B 1050 MET cc_start: 0.6648 (ptt) cc_final: 0.6366 (ptm) REVERT: B 1073 LYS cc_start: 0.5907 (mttt) cc_final: 0.5628 (mtpt) REVERT: B 1108 ASN cc_start: 0.7436 (m-40) cc_final: 0.7195 (m110) REVERT: B 1113 GLN cc_start: 0.6013 (mt0) cc_final: 0.5105 (mt0) REVERT: B 1118 ASP cc_start: 0.6314 (m-30) cc_final: 0.6058 (t0) REVERT: B 1119 ASN cc_start: 0.5381 (m-40) cc_final: 0.4732 (m110) REVERT: C 200 TYR cc_start: 0.5649 (m-80) cc_final: 0.5368 (m-80) REVERT: C 273 ARG cc_start: 0.4136 (mmt90) cc_final: 0.3719 (mmt-90) REVERT: C 309 GLU cc_start: 0.5082 (tp30) cc_final: 0.4552 (tt0) REVERT: C 340 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6947 (mp0) REVERT: C 383 CYS cc_start: 0.4851 (t) cc_final: 0.3918 (t) REVERT: C 528 LYS cc_start: 0.6116 (tttt) cc_final: 0.5303 (ttmm) REVERT: C 586 ASP cc_start: 0.5612 (m-30) cc_final: 0.5242 (m-30) REVERT: C 646 ARG cc_start: 0.6741 (mtm110) cc_final: 0.6056 (tmm160) REVERT: C 661 GLU cc_start: 0.5645 (mm-30) cc_final: 0.5410 (tp30) REVERT: C 663 ASP cc_start: 0.6843 (t0) cc_final: 0.6627 (t0) REVERT: C 675 GLN cc_start: 0.5041 (mt0) cc_final: 0.4623 (mt0) REVERT: C 702 GLU cc_start: 0.7371 (tt0) cc_final: 0.6778 (tp30) REVERT: C 776 LYS cc_start: 0.5327 (tttt) cc_final: 0.5112 (ttpp) REVERT: C 814 LYS cc_start: 0.5887 (mttt) cc_final: 0.5308 (mtpt) REVERT: C 823 PHE cc_start: 0.5832 (m-80) cc_final: 0.5616 (m-80) REVERT: C 902 MET cc_start: 0.6698 (mmm) cc_final: 0.6205 (tpt) REVERT: C 907 ASN cc_start: 0.6306 (OUTLIER) cc_final: 0.6056 (m110) REVERT: C 990 GLU cc_start: 0.4628 (mt-10) cc_final: 0.4021 (mp0) REVERT: C 1010 GLN cc_start: 0.4773 (mm-40) cc_final: 0.4049 (mt0) REVERT: C 1045 LYS cc_start: 0.6168 (ttpp) cc_final: 0.5933 (tmtp) outliers start: 24 outliers final: 6 residues processed: 392 average time/residue: 1.0602 time to fit residues: 493.1571 Evaluate side-chains 275 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 268 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 122 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 228 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 264 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A1002 GLN A1088 HIS B 30 ASN B 207 HIS B 606 ASN B 955 ASN B1101 HIS C 196 ASN C 207 HIS C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN C 764 ASN C1119 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.221645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.175449 restraints weight = 22098.878| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.57 r_work: 0.3559 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23364 Z= 0.138 Angle : 0.626 9.509 31818 Z= 0.335 Chirality : 0.047 0.222 3633 Planarity : 0.004 0.035 4107 Dihedral : 5.873 52.088 3107 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.32 % Favored : 97.64 % Rotamer: Outliers : 1.64 % Allowed : 7.10 % Favored : 91.27 % 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: -0.11 (0.15), residues: 2844 helix: 1.26 (0.20), residues: 666 sheet: -0.19 (0.19), residues: 631 loop : -0.57 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 64 HIS 0.003 0.001 HIS B1088 PHE 0.027 0.002 PHE B 168 TYR 0.024 0.002 TYR B 170 ARG 0.004 0.000 ARG C 567 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 1021) hydrogen bonds : angle 6.35711 ( 2826) SS BOND : bond 0.00318 ( 39) SS BOND : angle 1.43278 ( 78) covalent geometry : bond 0.00307 (23325) covalent geometry : angle 0.62236 (31740) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 306 time to evaluate : 2.494 Fit side-chains REVERT: A 239 GLN cc_start: 0.7343 (tt0) cc_final: 0.6805 (tt0) REVERT: A 305 SER cc_start: 0.9093 (t) cc_final: 0.8878 (p) REVERT: A 307 THR cc_start: 0.7737 (m) cc_final: 0.7392 (p) REVERT: A 378 LYS cc_start: 0.7080 (tptp) cc_final: 0.6605 (pttm) REVERT: A 532 ASN cc_start: 0.7961 (t0) cc_final: 0.7664 (m-40) REVERT: A 656 VAL cc_start: 0.7860 (t) cc_final: 0.7633 (m) REVERT: A 661 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7413 (mm-30) REVERT: A 674 TYR cc_start: 0.8563 (t80) cc_final: 0.8352 (t80) REVERT: A 779 GLN cc_start: 0.7836 (tp40) cc_final: 0.7458 (tp40) REVERT: A 814 LYS cc_start: 0.7402 (mttp) cc_final: 0.7102 (mtpp) REVERT: A 854 LYS cc_start: 0.3972 (mttp) cc_final: 0.3290 (ptmt) REVERT: A 988 GLU cc_start: 0.7578 (tp30) cc_final: 0.6627 (mp0) REVERT: A 1010 GLN cc_start: 0.7479 (mt0) cc_final: 0.7188 (mm-40) REVERT: A 1092 GLU cc_start: 0.6894 (mp0) cc_final: 0.6498 (mt-10) REVERT: A 1107 ARG cc_start: 0.7811 (mtm180) cc_final: 0.7504 (mtt180) REVERT: B 271 GLN cc_start: 0.8166 (mt0) cc_final: 0.7407 (mp10) REVERT: B 278 LYS cc_start: 0.7667 (tttt) cc_final: 0.7245 (ttmm) REVERT: B 287 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6913 (t0) REVERT: B 314 GLN cc_start: 0.8589 (tt0) cc_final: 0.8312 (tp40) REVERT: B 317 ASN cc_start: 0.8441 (m-40) cc_final: 0.8068 (m110) REVERT: B 388 ASN cc_start: 0.8019 (m110) cc_final: 0.7622 (m-40) REVERT: B 569 ILE cc_start: 0.7805 (mm) cc_final: 0.7503 (tt) REVERT: B 612 TYR cc_start: 0.8568 (m-80) cc_final: 0.8256 (m-80) REVERT: B 613 GLN cc_start: 0.8587 (mt0) cc_final: 0.8356 (mt0) REVERT: B 646 ARG cc_start: 0.7260 (ttm170) cc_final: 0.6523 (tpt170) REVERT: B 697 MET cc_start: 0.8648 (ptm) cc_final: 0.8407 (ptp) REVERT: B 735 SER cc_start: 0.8435 (t) cc_final: 0.8211 (p) REVERT: B 790 LYS cc_start: 0.8586 (pttt) cc_final: 0.8228 (ptmm) REVERT: B 814 LYS cc_start: 0.7196 (mttt) cc_final: 0.6382 (mmmt) REVERT: B 957 GLN cc_start: 0.7569 (tp-100) cc_final: 0.7305 (tt0) REVERT: B 988 GLU cc_start: 0.7260 (tp30) cc_final: 0.6315 (mp0) REVERT: B 998 THR cc_start: 0.8596 (m) cc_final: 0.8377 (m) REVERT: B 1010 GLN cc_start: 0.7402 (mm-40) cc_final: 0.6708 (tt0) REVERT: B 1045 LYS cc_start: 0.8117 (ttpp) cc_final: 0.7555 (mptt) REVERT: B 1113 GLN cc_start: 0.8026 (mt0) cc_final: 0.7396 (mt0) REVERT: B 1118 ASP cc_start: 0.7828 (m-30) cc_final: 0.7603 (t0) REVERT: B 1119 ASN cc_start: 0.6819 (m-40) cc_final: 0.6471 (m110) REVERT: C 273 ARG cc_start: 0.6566 (mmt90) cc_final: 0.6121 (mmt-90) REVERT: C 305 SER cc_start: 0.8807 (t) cc_final: 0.8445 (p) REVERT: C 340 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7611 (mp0) REVERT: C 396 TYR cc_start: 0.7114 (m-80) cc_final: 0.6095 (m-80) REVERT: C 424 LYS cc_start: 0.6522 (tptp) cc_final: 0.5753 (tptt) REVERT: C 528 LYS cc_start: 0.7263 (tttt) cc_final: 0.6637 (ttmm) REVERT: C 567 ARG cc_start: 0.6133 (mtt-85) cc_final: 0.5810 (mmm-85) REVERT: C 675 GLN cc_start: 0.7258 (mt0) cc_final: 0.6947 (mt0) REVERT: C 745 ASP cc_start: 0.7011 (p0) cc_final: 0.6800 (p0) REVERT: C 814 LYS cc_start: 0.7476 (mttt) cc_final: 0.6969 (mtpt) REVERT: C 990 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6566 (mp0) REVERT: C 994 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7445 (m-30) REVERT: C 1010 GLN cc_start: 0.7627 (mm-40) cc_final: 0.6988 (tt0) outliers start: 42 outliers final: 16 residues processed: 333 average time/residue: 0.9482 time to fit residues: 381.1495 Evaluate side-chains 256 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 238 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 140 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 233 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 267 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 422 ASN A 613 GLN B 334 ASN B 394 ASN B 907 ASN B 914 ASN C 394 ASN C 907 ASN C1088 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.215215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.169247 restraints weight = 22107.013| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.93 r_work: 0.3451 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 23364 Z= 0.246 Angle : 0.659 11.214 31818 Z= 0.347 Chirality : 0.049 0.181 3633 Planarity : 0.005 0.041 4107 Dihedral : 5.497 39.452 3102 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.69 % Allowed : 8.73 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 2844 helix: 1.10 (0.20), residues: 679 sheet: -0.43 (0.19), residues: 672 loop : -0.70 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 64 HIS 0.007 0.001 HIS C1064 PHE 0.027 0.002 PHE B 168 TYR 0.025 0.002 TYR B1067 ARG 0.011 0.001 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.04679 ( 1021) hydrogen bonds : angle 6.23494 ( 2826) SS BOND : bond 0.00615 ( 39) SS BOND : angle 2.04172 ( 78) covalent geometry : bond 0.00610 (23325) covalent geometry : angle 0.65235 (31740) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 244 time to evaluate : 2.437 Fit side-chains REVERT: A 47 VAL cc_start: 0.7920 (OUTLIER) cc_final: 0.7565 (p) REVERT: A 58 PHE cc_start: 0.7992 (m-10) cc_final: 0.7728 (m-10) REVERT: A 228 ASP cc_start: 0.6378 (t0) cc_final: 0.6066 (t0) REVERT: A 239 GLN cc_start: 0.7439 (tt0) cc_final: 0.6939 (tt0) REVERT: A 305 SER cc_start: 0.9123 (t) cc_final: 0.8902 (p) REVERT: A 532 ASN cc_start: 0.8038 (t0) cc_final: 0.7769 (m-40) REVERT: A 603 ASN cc_start: 0.7400 (t0) cc_final: 0.7119 (m-40) REVERT: A 616 ASN cc_start: 0.6170 (m-40) cc_final: 0.5572 (m-40) REVERT: A 661 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7510 (mm-30) REVERT: A 779 GLN cc_start: 0.7846 (tp40) cc_final: 0.7450 (tp40) REVERT: A 814 LYS cc_start: 0.7378 (mttp) cc_final: 0.7042 (mtpp) REVERT: A 854 LYS cc_start: 0.4266 (mttp) cc_final: 0.3596 (ptmt) REVERT: A 988 GLU cc_start: 0.7439 (tp30) cc_final: 0.6566 (mp0) REVERT: A 1010 GLN cc_start: 0.7494 (mt0) cc_final: 0.7246 (mm-40) REVERT: A 1092 GLU cc_start: 0.7002 (mp0) cc_final: 0.6565 (mt-10) REVERT: A 1107 ARG cc_start: 0.7989 (mtm180) cc_final: 0.7646 (mtt180) REVERT: A 1128 VAL cc_start: 0.8474 (t) cc_final: 0.8106 (p) REVERT: B 271 GLN cc_start: 0.8076 (mt0) cc_final: 0.7537 (mt0) REVERT: B 314 GLN cc_start: 0.8736 (tt0) cc_final: 0.8488 (tp40) REVERT: B 534 VAL cc_start: 0.8308 (t) cc_final: 0.8095 (m) REVERT: B 564 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.5847 (mm-40) REVERT: B 569 ILE cc_start: 0.7989 (mm) cc_final: 0.7664 (tt) REVERT: B 572 THR cc_start: 0.7895 (t) cc_final: 0.7577 (t) REVERT: B 612 TYR cc_start: 0.8722 (m-80) cc_final: 0.8276 (m-80) REVERT: B 613 GLN cc_start: 0.8615 (mt0) cc_final: 0.8320 (mt0) REVERT: B 646 ARG cc_start: 0.7430 (ttm170) cc_final: 0.6574 (tpt170) REVERT: B 790 LYS cc_start: 0.8617 (pttt) cc_final: 0.8283 (ptmm) REVERT: B 814 LYS cc_start: 0.7237 (mttt) cc_final: 0.6407 (mmmt) REVERT: B 957 GLN cc_start: 0.7658 (tp-100) cc_final: 0.7410 (tt0) REVERT: B 988 GLU cc_start: 0.7360 (tp30) cc_final: 0.6473 (mp0) REVERT: B 994 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.6965 (m-30) REVERT: B 998 THR cc_start: 0.8560 (m) cc_final: 0.8198 (m) REVERT: B 1010 GLN cc_start: 0.7493 (mm-40) cc_final: 0.6753 (tt0) REVERT: B 1045 LYS cc_start: 0.8217 (ttpp) cc_final: 0.7591 (mptp) REVERT: B 1113 GLN cc_start: 0.8017 (mt0) cc_final: 0.7287 (mt0) REVERT: B 1118 ASP cc_start: 0.8002 (m-30) cc_final: 0.7665 (t0) REVERT: B 1139 ASP cc_start: 0.7550 (t0) cc_final: 0.7168 (m-30) REVERT: C 271 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7181 (mp10) REVERT: C 273 ARG cc_start: 0.6589 (mmt90) cc_final: 0.6132 (mmt-90) REVERT: C 305 SER cc_start: 0.8932 (t) cc_final: 0.8584 (p) REVERT: C 340 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7615 (mp0) REVERT: C 392 PHE cc_start: 0.7210 (m-80) cc_final: 0.6981 (m-80) REVERT: C 394 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7019 (p0) REVERT: C 396 TYR cc_start: 0.7450 (m-80) cc_final: 0.6682 (m-80) REVERT: C 424 LYS cc_start: 0.6592 (tptp) cc_final: 0.6337 (tptp) REVERT: C 516 GLU cc_start: 0.7670 (tp30) cc_final: 0.7123 (mt-10) REVERT: C 528 LYS cc_start: 0.7191 (tttt) cc_final: 0.6559 (tppt) REVERT: C 567 ARG cc_start: 0.6282 (mtt-85) cc_final: 0.5911 (mmm-85) REVERT: C 574 ASP cc_start: 0.7907 (t0) cc_final: 0.7686 (t0) REVERT: C 646 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6667 (ttm110) REVERT: C 675 GLN cc_start: 0.7328 (mt0) cc_final: 0.6944 (mt0) REVERT: C 745 ASP cc_start: 0.7208 (p0) cc_final: 0.6976 (p0) REVERT: C 764 ASN cc_start: 0.8153 (m-40) cc_final: 0.7953 (m110) REVERT: C 814 LYS cc_start: 0.7438 (mttt) cc_final: 0.6915 (mtpt) REVERT: C 990 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6613 (mp0) REVERT: C 994 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7576 (m-30) REVERT: C 1010 GLN cc_start: 0.7639 (mm-40) cc_final: 0.6863 (pt0) REVERT: C 1127 ASP cc_start: 0.7304 (m-30) cc_final: 0.7093 (m-30) outliers start: 69 outliers final: 35 residues processed: 288 average time/residue: 0.9935 time to fit residues: 347.8450 Evaluate side-chains 265 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 4.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 217 optimal weight: 0.0980 chunk 47 optimal weight: 6.9990 chunk 265 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 394 ASN A 762 GLN B 394 ASN B 641 ASN C 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1058 HIS C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.219716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.173820 restraints weight = 22290.192| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.84 r_work: 0.3609 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23364 Z= 0.120 Angle : 0.537 9.254 31818 Z= 0.284 Chirality : 0.045 0.163 3633 Planarity : 0.004 0.037 4107 Dihedral : 4.919 34.806 3102 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.11 % Allowed : 10.41 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 2844 helix: 1.66 (0.20), residues: 681 sheet: -0.31 (0.19), residues: 642 loop : -0.61 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.003 0.001 HIS A1088 PHE 0.027 0.001 PHE B 168 TYR 0.024 0.001 TYR B 170 ARG 0.005 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 1021) hydrogen bonds : angle 5.75769 ( 2826) SS BOND : bond 0.00346 ( 39) SS BOND : angle 1.74306 ( 78) covalent geometry : bond 0.00276 (23325) covalent geometry : angle 0.53035 (31740) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 262 time to evaluate : 2.460 Fit side-chains REVERT: A 47 VAL cc_start: 0.7986 (t) cc_final: 0.7676 (p) REVERT: A 88 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6237 (t0) REVERT: A 200 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.6263 (t80) REVERT: A 239 GLN cc_start: 0.7489 (tt0) cc_final: 0.7014 (tt0) REVERT: A 378 LYS cc_start: 0.7226 (tptp) cc_final: 0.6825 (pttm) REVERT: A 532 ASN cc_start: 0.8066 (t0) cc_final: 0.7785 (m-40) REVERT: A 661 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7532 (mm-30) REVERT: A 779 GLN cc_start: 0.7808 (tp40) cc_final: 0.7416 (tp40) REVERT: A 814 LYS cc_start: 0.7512 (mttp) cc_final: 0.7213 (mtpp) REVERT: A 854 LYS cc_start: 0.4195 (mttp) cc_final: 0.3527 (ptpt) REVERT: A 988 GLU cc_start: 0.7297 (tp30) cc_final: 0.6592 (mp0) REVERT: A 1010 GLN cc_start: 0.7549 (mt0) cc_final: 0.7320 (mm-40) REVERT: A 1092 GLU cc_start: 0.6858 (mp0) cc_final: 0.6573 (mt-10) REVERT: A 1107 ARG cc_start: 0.7780 (mtm180) cc_final: 0.7513 (mtt180) REVERT: A 1128 VAL cc_start: 0.8520 (t) cc_final: 0.8168 (p) REVERT: B 271 GLN cc_start: 0.7982 (mt0) cc_final: 0.7163 (mp10) REVERT: B 314 GLN cc_start: 0.8494 (tt0) cc_final: 0.8282 (tp40) REVERT: B 317 ASN cc_start: 0.8398 (m-40) cc_final: 0.7986 (m110) REVERT: B 324 GLU cc_start: 0.6612 (pt0) cc_final: 0.6075 (pm20) REVERT: B 534 VAL cc_start: 0.8273 (t) cc_final: 0.8057 (m) REVERT: B 569 ILE cc_start: 0.7920 (mm) cc_final: 0.7537 (tt) REVERT: B 572 THR cc_start: 0.7924 (t) cc_final: 0.7592 (t) REVERT: B 612 TYR cc_start: 0.8650 (m-80) cc_final: 0.8336 (m-80) REVERT: B 613 GLN cc_start: 0.8570 (mt0) cc_final: 0.8350 (mt0) REVERT: B 646 ARG cc_start: 0.7337 (ttm170) cc_final: 0.6646 (tpt170) REVERT: B 779 GLN cc_start: 0.7495 (tp40) cc_final: 0.7114 (tt0) REVERT: B 790 LYS cc_start: 0.8609 (pttt) cc_final: 0.8403 (ptmm) REVERT: B 814 LYS cc_start: 0.7214 (mttt) cc_final: 0.6353 (mmmt) REVERT: B 988 GLU cc_start: 0.7311 (tp30) cc_final: 0.6480 (mp0) REVERT: B 994 ASP cc_start: 0.7187 (OUTLIER) cc_final: 0.6700 (m-30) REVERT: B 998 THR cc_start: 0.8496 (m) cc_final: 0.8195 (m) REVERT: B 1010 GLN cc_start: 0.7402 (mm-40) cc_final: 0.6649 (pt0) REVERT: B 1045 LYS cc_start: 0.8130 (ttpp) cc_final: 0.7548 (mptt) REVERT: B 1094 VAL cc_start: 0.7987 (m) cc_final: 0.7718 (p) REVERT: B 1113 GLN cc_start: 0.7944 (mt0) cc_final: 0.7289 (mt0) REVERT: B 1118 ASP cc_start: 0.8006 (m-30) cc_final: 0.7653 (t0) REVERT: B 1139 ASP cc_start: 0.7589 (t0) cc_final: 0.7145 (m-30) REVERT: C 84 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6339 (mt) REVERT: C 287 ASP cc_start: 0.7797 (m-30) cc_final: 0.7510 (m-30) REVERT: C 305 SER cc_start: 0.8891 (t) cc_final: 0.8659 (p) REVERT: C 378 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7492 (ttmt) REVERT: C 396 TYR cc_start: 0.7349 (m-80) cc_final: 0.6754 (m-80) REVERT: C 424 LYS cc_start: 0.6688 (tptp) cc_final: 0.6083 (tptp) REVERT: C 516 GLU cc_start: 0.7757 (tp30) cc_final: 0.7326 (mt-10) REVERT: C 528 LYS cc_start: 0.7247 (tttt) cc_final: 0.6662 (tppt) REVERT: C 574 ASP cc_start: 0.7802 (t0) cc_final: 0.7512 (t0) REVERT: C 675 GLN cc_start: 0.7327 (mt0) cc_final: 0.6941 (mt0) REVERT: C 764 ASN cc_start: 0.8032 (m-40) cc_final: 0.7772 (m110) REVERT: C 814 LYS cc_start: 0.7550 (mttt) cc_final: 0.6978 (mtpt) REVERT: C 950 ASP cc_start: 0.8285 (m-30) cc_final: 0.7997 (m-30) REVERT: C 994 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: C 1010 GLN cc_start: 0.7578 (mm-40) cc_final: 0.6989 (tt0) outliers start: 54 outliers final: 26 residues processed: 301 average time/residue: 0.8792 time to fit residues: 324.9477 Evaluate side-chains 256 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 3.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 280 optimal weight: 0.0570 chunk 42 optimal weight: 3.9990 chunk 165 optimal weight: 0.0470 chunk 272 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 262 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 231 optimal weight: 0.0770 chunk 146 optimal weight: 3.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 394 ASN B 30 ASN B 394 ASN B1119 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.217159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155319 restraints weight = 22441.402| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.88 r_work: 0.3737 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23364 Z= 0.107 Angle : 0.505 8.264 31818 Z= 0.266 Chirality : 0.044 0.157 3633 Planarity : 0.004 0.039 4107 Dihedral : 4.533 33.280 3102 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.50 % Allowed : 10.99 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 2844 helix: 1.96 (0.20), residues: 674 sheet: -0.25 (0.19), residues: 634 loop : -0.60 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.003 0.001 HIS A1088 PHE 0.021 0.001 PHE B 168 TYR 0.026 0.001 TYR B 170 ARG 0.004 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 1021) hydrogen bonds : angle 5.45973 ( 2826) SS BOND : bond 0.00270 ( 39) SS BOND : angle 1.68289 ( 78) covalent geometry : bond 0.00242 (23325) covalent geometry : angle 0.49856 (31740) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 263 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.7918 (t) cc_final: 0.7690 (p) REVERT: A 200 TYR cc_start: 0.6975 (OUTLIER) cc_final: 0.6556 (t80) REVERT: A 239 GLN cc_start: 0.7493 (tt0) cc_final: 0.7023 (tt0) REVERT: A 378 LYS cc_start: 0.7219 (tptp) cc_final: 0.6828 (pttm) REVERT: A 532 ASN cc_start: 0.7971 (t0) cc_final: 0.7708 (m-40) REVERT: A 661 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7596 (mm-30) REVERT: A 779 GLN cc_start: 0.7814 (tp40) cc_final: 0.7491 (tp40) REVERT: A 814 LYS cc_start: 0.7427 (mttp) cc_final: 0.7133 (mtpp) REVERT: A 854 LYS cc_start: 0.4394 (mttp) cc_final: 0.3673 (ptpt) REVERT: A 988 GLU cc_start: 0.7147 (tp30) cc_final: 0.6656 (mp0) REVERT: A 1092 GLU cc_start: 0.6710 (mp0) cc_final: 0.6425 (mt-10) REVERT: A 1128 VAL cc_start: 0.8449 (t) cc_final: 0.8111 (p) REVERT: B 52 GLN cc_start: 0.8371 (tt0) cc_final: 0.8040 (tp40) REVERT: B 271 GLN cc_start: 0.7970 (mt0) cc_final: 0.7225 (mp10) REVERT: B 317 ASN cc_start: 0.8288 (m-40) cc_final: 0.7884 (m110) REVERT: B 324 GLU cc_start: 0.6700 (pt0) cc_final: 0.6227 (pm20) REVERT: B 564 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.5800 (mm-40) REVERT: B 569 ILE cc_start: 0.7963 (mm) cc_final: 0.7618 (tt) REVERT: B 572 THR cc_start: 0.7769 (t) cc_final: 0.7493 (t) REVERT: B 583 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7452 (pt0) REVERT: B 612 TYR cc_start: 0.8579 (m-80) cc_final: 0.8333 (m-80) REVERT: B 613 GLN cc_start: 0.8509 (mt0) cc_final: 0.8301 (mt0) REVERT: B 646 ARG cc_start: 0.7240 (ttm170) cc_final: 0.6697 (tpt170) REVERT: B 698 SER cc_start: 0.8533 (t) cc_final: 0.8247 (p) REVERT: B 779 GLN cc_start: 0.7459 (tp40) cc_final: 0.7230 (tt0) REVERT: B 814 LYS cc_start: 0.7208 (mttt) cc_final: 0.6408 (mmmt) REVERT: B 988 GLU cc_start: 0.7385 (tp30) cc_final: 0.6645 (mp0) REVERT: B 994 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6504 (m-30) REVERT: B 998 THR cc_start: 0.8521 (m) cc_final: 0.8237 (m) REVERT: B 1010 GLN cc_start: 0.7299 (mm-40) cc_final: 0.6747 (pt0) REVERT: B 1045 LYS cc_start: 0.8130 (ttpp) cc_final: 0.7602 (mptp) REVERT: B 1113 GLN cc_start: 0.7962 (mt0) cc_final: 0.7371 (mt0) REVERT: B 1118 ASP cc_start: 0.7990 (m-30) cc_final: 0.7678 (t0) REVERT: C 84 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6234 (mt) REVERT: C 287 ASP cc_start: 0.7750 (m-30) cc_final: 0.7431 (m-30) REVERT: C 305 SER cc_start: 0.8747 (t) cc_final: 0.8527 (p) REVERT: C 378 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7441 (ttmt) REVERT: C 396 TYR cc_start: 0.7231 (m-80) cc_final: 0.6790 (m-80) REVERT: C 424 LYS cc_start: 0.6675 (tptp) cc_final: 0.6044 (tptp) REVERT: C 516 GLU cc_start: 0.7824 (tp30) cc_final: 0.7607 (tp30) REVERT: C 528 LYS cc_start: 0.7337 (tttt) cc_final: 0.6699 (tppt) REVERT: C 564 GLN cc_start: 0.7049 (tp40) cc_final: 0.6779 (mp-120) REVERT: C 675 GLN cc_start: 0.7320 (mt0) cc_final: 0.6976 (mt0) REVERT: C 704 SER cc_start: 0.8375 (p) cc_final: 0.8147 (t) REVERT: C 764 ASN cc_start: 0.8044 (m-40) cc_final: 0.7762 (m110) REVERT: C 814 LYS cc_start: 0.7546 (mttt) cc_final: 0.6988 (mtpt) REVERT: C 994 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7329 (m-30) REVERT: C 995 ARG cc_start: 0.7344 (mtt180) cc_final: 0.6909 (mtp180) REVERT: C 1010 GLN cc_start: 0.7523 (mm-40) cc_final: 0.7025 (tt0) REVERT: C 1119 ASN cc_start: 0.6988 (m-40) cc_final: 0.6689 (m-40) outliers start: 64 outliers final: 37 residues processed: 303 average time/residue: 0.9508 time to fit residues: 348.2238 Evaluate side-chains 274 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 230 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 174 optimal weight: 3.9990 chunk 266 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 256 optimal weight: 0.7980 chunk 222 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 127 optimal weight: 0.2980 chunk 231 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 762 GLN B 394 ASN B1088 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.217218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155318 restraints weight = 22298.787| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.88 r_work: 0.3639 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23364 Z= 0.111 Angle : 0.505 9.187 31818 Z= 0.265 Chirality : 0.044 0.157 3633 Planarity : 0.004 0.041 4107 Dihedral : 4.395 32.347 3100 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.50 % Allowed : 11.93 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 2844 helix: 2.05 (0.20), residues: 674 sheet: -0.21 (0.19), residues: 649 loop : -0.59 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A1088 PHE 0.017 0.001 PHE C 65 TYR 0.018 0.001 TYR B1067 ARG 0.004 0.000 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 1021) hydrogen bonds : angle 5.36797 ( 2826) SS BOND : bond 0.00360 ( 39) SS BOND : angle 1.88061 ( 78) covalent geometry : bond 0.00254 (23325) covalent geometry : angle 0.49695 (31740) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 247 time to evaluate : 2.371 Fit side-chains REVERT: A 47 VAL cc_start: 0.7892 (t) cc_final: 0.7689 (p) REVERT: A 88 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6267 (t0) REVERT: A 200 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.6561 (t80) REVERT: A 239 GLN cc_start: 0.7478 (tt0) cc_final: 0.7024 (tt0) REVERT: A 378 LYS cc_start: 0.7241 (tptp) cc_final: 0.6832 (pttm) REVERT: A 532 ASN cc_start: 0.7983 (t0) cc_final: 0.7680 (m-40) REVERT: A 558 LYS cc_start: 0.8022 (mptp) cc_final: 0.7415 (mmtt) REVERT: A 661 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7651 (mm-30) REVERT: A 779 GLN cc_start: 0.7819 (tp40) cc_final: 0.7450 (tp40) REVERT: A 814 LYS cc_start: 0.7435 (mttp) cc_final: 0.7199 (mtpt) REVERT: A 854 LYS cc_start: 0.4382 (mttp) cc_final: 0.3641 (ptpt) REVERT: A 988 GLU cc_start: 0.7134 (tp30) cc_final: 0.6684 (mp0) REVERT: A 1092 GLU cc_start: 0.6814 (mp0) cc_final: 0.6487 (mt-10) REVERT: A 1128 VAL cc_start: 0.8433 (t) cc_final: 0.8129 (p) REVERT: B 52 GLN cc_start: 0.8371 (tt0) cc_final: 0.8054 (tp40) REVERT: B 271 GLN cc_start: 0.7968 (mt0) cc_final: 0.7207 (mp10) REVERT: B 278 LYS cc_start: 0.7740 (tttt) cc_final: 0.7418 (ttpp) REVERT: B 317 ASN cc_start: 0.8247 (m-40) cc_final: 0.7875 (m110) REVERT: B 324 GLU cc_start: 0.6720 (pt0) cc_final: 0.6193 (pm20) REVERT: B 564 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.5842 (mm-40) REVERT: B 569 ILE cc_start: 0.7936 (mm) cc_final: 0.7581 (tt) REVERT: B 572 THR cc_start: 0.7789 (t) cc_final: 0.7508 (t) REVERT: B 612 TYR cc_start: 0.8589 (m-80) cc_final: 0.8272 (m-80) REVERT: B 646 ARG cc_start: 0.7256 (ttm170) cc_final: 0.6712 (tpt170) REVERT: B 698 SER cc_start: 0.8516 (t) cc_final: 0.8215 (p) REVERT: B 779 GLN cc_start: 0.7473 (tp40) cc_final: 0.7266 (tt0) REVERT: B 814 LYS cc_start: 0.7284 (mttt) cc_final: 0.6523 (mmmt) REVERT: B 988 GLU cc_start: 0.7369 (tp30) cc_final: 0.6647 (mp0) REVERT: B 994 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6539 (m-30) REVERT: B 998 THR cc_start: 0.8525 (m) cc_final: 0.8237 (m) REVERT: B 1010 GLN cc_start: 0.7314 (mm-40) cc_final: 0.6769 (pt0) REVERT: B 1045 LYS cc_start: 0.8110 (ttpp) cc_final: 0.7574 (mptp) REVERT: B 1113 GLN cc_start: 0.7974 (mt0) cc_final: 0.7390 (mt0) REVERT: B 1118 ASP cc_start: 0.7977 (m-30) cc_final: 0.7647 (t0) REVERT: C 84 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6308 (mt) REVERT: C 287 ASP cc_start: 0.7788 (m-30) cc_final: 0.7425 (m-30) REVERT: C 305 SER cc_start: 0.8731 (t) cc_final: 0.8522 (p) REVERT: C 317 ASN cc_start: 0.8039 (t0) cc_final: 0.7693 (t0) REVERT: C 378 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7440 (ttmt) REVERT: C 396 TYR cc_start: 0.7199 (m-80) cc_final: 0.6749 (m-80) REVERT: C 424 LYS cc_start: 0.6565 (tptp) cc_final: 0.6131 (tptp) REVERT: C 516 GLU cc_start: 0.7800 (tp30) cc_final: 0.7595 (tp30) REVERT: C 528 LYS cc_start: 0.7246 (tttt) cc_final: 0.6633 (tppt) REVERT: C 564 GLN cc_start: 0.7099 (tp40) cc_final: 0.6812 (mp-120) REVERT: C 643 PHE cc_start: 0.6213 (t80) cc_final: 0.5863 (t80) REVERT: C 675 GLN cc_start: 0.7308 (mt0) cc_final: 0.6961 (mt0) REVERT: C 790 LYS cc_start: 0.8275 (pttt) cc_final: 0.7392 (mtpt) REVERT: C 814 LYS cc_start: 0.7521 (mttt) cc_final: 0.7026 (mtpt) REVERT: C 994 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7339 (m-30) REVERT: C 995 ARG cc_start: 0.7451 (mtt180) cc_final: 0.6975 (mtp180) REVERT: C 1010 GLN cc_start: 0.7507 (mm-40) cc_final: 0.6977 (pt0) REVERT: C 1136 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8614 (t) outliers start: 64 outliers final: 31 residues processed: 288 average time/residue: 0.9045 time to fit residues: 320.4430 Evaluate side-chains 270 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 23 optimal weight: 8.9990 chunk 241 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 195 optimal weight: 0.7980 chunk 273 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 282 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 935 GLN B 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.213153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.153497 restraints weight = 22337.204| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.89 r_work: 0.3592 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23364 Z= 0.181 Angle : 0.558 9.069 31818 Z= 0.291 Chirality : 0.046 0.158 3633 Planarity : 0.004 0.042 4107 Dihedral : 4.562 32.770 3099 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.61 % Allowed : 12.24 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 2844 helix: 1.74 (0.20), residues: 678 sheet: -0.38 (0.19), residues: 630 loop : -0.62 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.004 0.001 HIS C1064 PHE 0.021 0.002 PHE A 192 TYR 0.026 0.001 TYR B 170 ARG 0.004 0.000 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.03877 ( 1021) hydrogen bonds : angle 5.58434 ( 2826) SS BOND : bond 0.00399 ( 39) SS BOND : angle 2.02283 ( 78) covalent geometry : bond 0.00445 (23325) covalent geometry : angle 0.54977 (31740) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 227 time to evaluate : 2.522 Fit side-chains REVERT: A 47 VAL cc_start: 0.7794 (t) cc_final: 0.7539 (p) REVERT: A 200 TYR cc_start: 0.6884 (OUTLIER) cc_final: 0.5633 (t80) REVERT: A 239 GLN cc_start: 0.7352 (tt0) cc_final: 0.6825 (tt0) REVERT: A 351 TYR cc_start: 0.5143 (p90) cc_final: 0.4458 (p90) REVERT: A 378 LYS cc_start: 0.7101 (tptp) cc_final: 0.6693 (pttm) REVERT: A 532 ASN cc_start: 0.7983 (t0) cc_final: 0.7649 (m-40) REVERT: A 584 ILE cc_start: 0.8024 (mt) cc_final: 0.7817 (mt) REVERT: A 661 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7523 (mm-30) REVERT: A 779 GLN cc_start: 0.7706 (tp40) cc_final: 0.7186 (tt0) REVERT: A 814 LYS cc_start: 0.7362 (mttp) cc_final: 0.7026 (mtpt) REVERT: A 854 LYS cc_start: 0.4242 (mttp) cc_final: 0.3543 (ptpt) REVERT: A 969 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7785 (m-40) REVERT: A 988 GLU cc_start: 0.7035 (tp30) cc_final: 0.6535 (mp0) REVERT: A 1092 GLU cc_start: 0.6987 (mp0) cc_final: 0.6629 (mt-10) REVERT: A 1128 VAL cc_start: 0.8443 (t) cc_final: 0.8067 (p) REVERT: B 52 GLN cc_start: 0.8387 (tt0) cc_final: 0.8029 (tp40) REVERT: B 231 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7736 (pp) REVERT: B 271 GLN cc_start: 0.7881 (mt0) cc_final: 0.7019 (mp10) REVERT: B 564 GLN cc_start: 0.6734 (OUTLIER) cc_final: 0.5751 (mm-40) REVERT: B 569 ILE cc_start: 0.7946 (mm) cc_final: 0.7512 (tt) REVERT: B 572 THR cc_start: 0.7608 (t) cc_final: 0.7328 (t) REVERT: B 583 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7491 (pt0) REVERT: B 612 TYR cc_start: 0.8579 (m-80) cc_final: 0.8295 (m-80) REVERT: B 646 ARG cc_start: 0.7240 (ttm170) cc_final: 0.6596 (tpt170) REVERT: B 698 SER cc_start: 0.8522 (t) cc_final: 0.8138 (p) REVERT: B 814 LYS cc_start: 0.7294 (mttt) cc_final: 0.6403 (mmmt) REVERT: B 988 GLU cc_start: 0.7230 (tp30) cc_final: 0.6443 (mp0) REVERT: B 994 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6514 (m-30) REVERT: B 998 THR cc_start: 0.8381 (m) cc_final: 0.8040 (m) REVERT: B 1010 GLN cc_start: 0.7272 (mm-40) cc_final: 0.6580 (pt0) REVERT: B 1045 LYS cc_start: 0.8136 (ttpp) cc_final: 0.7525 (mptp) REVERT: B 1118 ASP cc_start: 0.7899 (m-30) cc_final: 0.7511 (t0) REVERT: C 84 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6071 (mt) REVERT: C 281 GLU cc_start: 0.7539 (pm20) cc_final: 0.7288 (pt0) REVERT: C 287 ASP cc_start: 0.7802 (m-30) cc_final: 0.7419 (m-30) REVERT: C 305 SER cc_start: 0.8836 (t) cc_final: 0.8604 (p) REVERT: C 317 ASN cc_start: 0.8145 (t0) cc_final: 0.7831 (t0) REVERT: C 364 ASP cc_start: 0.7716 (t0) cc_final: 0.7118 (t0) REVERT: C 378 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7408 (mtmt) REVERT: C 396 TYR cc_start: 0.7078 (m-80) cc_final: 0.6587 (m-80) REVERT: C 424 LYS cc_start: 0.6396 (tptp) cc_final: 0.5680 (tptp) REVERT: C 516 GLU cc_start: 0.7734 (tp30) cc_final: 0.7414 (tp30) REVERT: C 528 LYS cc_start: 0.7139 (tttt) cc_final: 0.6478 (tppt) REVERT: C 564 GLN cc_start: 0.7071 (tp40) cc_final: 0.6706 (mp-120) REVERT: C 643 PHE cc_start: 0.6337 (t80) cc_final: 0.6103 (t80) REVERT: C 675 GLN cc_start: 0.7386 (mt0) cc_final: 0.6955 (mt0) REVERT: C 790 LYS cc_start: 0.8334 (pttt) cc_final: 0.7367 (mtpt) REVERT: C 814 LYS cc_start: 0.7464 (mttt) cc_final: 0.6882 (mtpt) REVERT: C 950 ASP cc_start: 0.8206 (m-30) cc_final: 0.7879 (m-30) REVERT: C 990 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6346 (mp0) REVERT: C 994 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7205 (m-30) REVERT: C 995 ARG cc_start: 0.7374 (mtt180) cc_final: 0.6801 (mtp180) REVERT: C 1010 GLN cc_start: 0.7452 (mm-40) cc_final: 0.6806 (pt0) outliers start: 67 outliers final: 37 residues processed: 270 average time/residue: 0.9377 time to fit residues: 310.0826 Evaluate side-chains 262 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 CYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 53 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 256 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 36 optimal weight: 30.0000 chunk 158 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 231 optimal weight: 20.0000 chunk 282 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B1088 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.216294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.157877 restraints weight = 22245.054| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.87 r_work: 0.3630 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23364 Z= 0.116 Angle : 0.509 8.716 31818 Z= 0.266 Chirality : 0.044 0.186 3633 Planarity : 0.004 0.043 4107 Dihedral : 4.342 31.780 3099 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.03 % Allowed : 12.98 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 2844 helix: 1.86 (0.20), residues: 684 sheet: -0.27 (0.19), residues: 613 loop : -0.57 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS B1088 PHE 0.031 0.001 PHE B 168 TYR 0.019 0.001 TYR B1067 ARG 0.003 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 1021) hydrogen bonds : angle 5.38059 ( 2826) SS BOND : bond 0.00343 ( 39) SS BOND : angle 1.88120 ( 78) covalent geometry : bond 0.00271 (23325) covalent geometry : angle 0.50093 (31740) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 233 time to evaluate : 2.452 Fit side-chains REVERT: A 47 VAL cc_start: 0.7983 (t) cc_final: 0.7755 (p) REVERT: A 54 LEU cc_start: 0.7592 (mp) cc_final: 0.7331 (mm) REVERT: A 88 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6227 (t0) REVERT: A 200 TYR cc_start: 0.6990 (OUTLIER) cc_final: 0.5843 (t80) REVERT: A 239 GLN cc_start: 0.7549 (tt0) cc_final: 0.7056 (tt0) REVERT: A 269 TYR cc_start: 0.7917 (m-80) cc_final: 0.7464 (m-80) REVERT: A 351 TYR cc_start: 0.5216 (p90) cc_final: 0.4531 (p90) REVERT: A 378 LYS cc_start: 0.7325 (tptp) cc_final: 0.6972 (pttm) REVERT: A 532 ASN cc_start: 0.8061 (t0) cc_final: 0.7715 (m-40) REVERT: A 661 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7684 (mm-30) REVERT: A 779 GLN cc_start: 0.7749 (tp40) cc_final: 0.7418 (tt0) REVERT: A 814 LYS cc_start: 0.7515 (mttp) cc_final: 0.7232 (mtpt) REVERT: A 854 LYS cc_start: 0.4563 (mttp) cc_final: 0.3850 (ptpt) REVERT: A 988 GLU cc_start: 0.7077 (tp30) cc_final: 0.6747 (mp0) REVERT: A 995 ARG cc_start: 0.7538 (mtt180) cc_final: 0.7023 (mtp180) REVERT: A 1092 GLU cc_start: 0.7037 (mp0) cc_final: 0.6659 (mt-10) REVERT: A 1128 VAL cc_start: 0.8414 (t) cc_final: 0.8093 (p) REVERT: B 52 GLN cc_start: 0.8363 (tt0) cc_final: 0.8095 (tp40) REVERT: B 271 GLN cc_start: 0.8018 (mt0) cc_final: 0.7283 (mp10) REVERT: B 564 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.5891 (mm-40) REVERT: B 568 ASP cc_start: 0.7528 (t0) cc_final: 0.7284 (m-30) REVERT: B 569 ILE cc_start: 0.7990 (mm) cc_final: 0.7618 (tt) REVERT: B 572 THR cc_start: 0.7711 (t) cc_final: 0.7398 (t) REVERT: B 583 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7556 (pt0) REVERT: B 612 TYR cc_start: 0.8621 (m-80) cc_final: 0.8371 (m-80) REVERT: B 646 ARG cc_start: 0.7291 (ttm170) cc_final: 0.6792 (tpt170) REVERT: B 698 SER cc_start: 0.8391 (t) cc_final: 0.8158 (p) REVERT: B 814 LYS cc_start: 0.7365 (mttt) cc_final: 0.6603 (mmmt) REVERT: B 988 GLU cc_start: 0.7409 (tp30) cc_final: 0.6783 (mp0) REVERT: B 994 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6608 (m-30) REVERT: B 998 THR cc_start: 0.8596 (m) cc_final: 0.8313 (m) REVERT: B 1010 GLN cc_start: 0.7348 (mm-40) cc_final: 0.6901 (pt0) REVERT: B 1045 LYS cc_start: 0.8131 (ttpp) cc_final: 0.7617 (mptt) REVERT: B 1113 GLN cc_start: 0.7902 (mt0) cc_final: 0.7402 (mt0) REVERT: B 1118 ASP cc_start: 0.7977 (m-30) cc_final: 0.7639 (t0) REVERT: C 84 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6413 (mt) REVERT: C 287 ASP cc_start: 0.7882 (m-30) cc_final: 0.7513 (m-30) REVERT: C 317 ASN cc_start: 0.8020 (t0) cc_final: 0.7659 (t0) REVERT: C 364 ASP cc_start: 0.7876 (t0) cc_final: 0.7329 (t0) REVERT: C 378 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7551 (ttmt) REVERT: C 396 TYR cc_start: 0.7402 (m-80) cc_final: 0.6956 (m-80) REVERT: C 424 LYS cc_start: 0.6590 (tptp) cc_final: 0.6106 (tptp) REVERT: C 516 GLU cc_start: 0.7854 (tp30) cc_final: 0.7588 (tp30) REVERT: C 528 LYS cc_start: 0.7260 (tttt) cc_final: 0.6666 (tppt) REVERT: C 564 GLN cc_start: 0.7148 (tp40) cc_final: 0.6937 (mp-120) REVERT: C 643 PHE cc_start: 0.6283 (t80) cc_final: 0.5938 (t80) REVERT: C 675 GLN cc_start: 0.7395 (mt0) cc_final: 0.7078 (mt0) REVERT: C 790 LYS cc_start: 0.8278 (pttt) cc_final: 0.7420 (mtpt) REVERT: C 814 LYS cc_start: 0.7549 (mttt) cc_final: 0.7084 (mtpt) REVERT: C 990 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6741 (mp0) REVERT: C 994 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7428 (m-30) REVERT: C 995 ARG cc_start: 0.7502 (mtt180) cc_final: 0.7113 (mtp180) REVERT: C 1010 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7136 (tt0) REVERT: C 1136 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8640 (t) REVERT: C 1145 LEU cc_start: 0.4079 (OUTLIER) cc_final: 0.3505 (pp) outliers start: 52 outliers final: 30 residues processed: 266 average time/residue: 0.9107 time to fit residues: 298.2802 Evaluate side-chains 259 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 985 CYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 226 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 229 optimal weight: 0.8980 chunk 201 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN B 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.215911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.153684 restraints weight = 22278.100| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.86 r_work: 0.3725 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 23364 Z= 0.127 Angle : 0.519 11.946 31818 Z= 0.270 Chirality : 0.044 0.195 3633 Planarity : 0.004 0.044 4107 Dihedral : 4.317 31.630 3099 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.87 % Allowed : 13.57 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 2844 helix: 1.96 (0.20), residues: 675 sheet: -0.23 (0.19), residues: 611 loop : -0.54 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.003 0.001 HIS A1088 PHE 0.025 0.001 PHE B 168 TYR 0.020 0.001 TYR B1067 ARG 0.003 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 1021) hydrogen bonds : angle 5.37761 ( 2826) SS BOND : bond 0.00348 ( 39) SS BOND : angle 2.15178 ( 78) covalent geometry : bond 0.00301 (23325) covalent geometry : angle 0.50871 (31740) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 2.370 Fit side-chains REVERT: A 47 VAL cc_start: 0.7838 (t) cc_final: 0.7600 (p) REVERT: A 88 ASP cc_start: 0.6922 (OUTLIER) cc_final: 0.6295 (t0) REVERT: A 200 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.5896 (t80) REVERT: A 239 GLN cc_start: 0.7409 (tt0) cc_final: 0.6894 (tt0) REVERT: A 351 TYR cc_start: 0.5238 (p90) cc_final: 0.4533 (p90) REVERT: A 378 LYS cc_start: 0.7246 (tptp) cc_final: 0.6868 (pttm) REVERT: A 532 ASN cc_start: 0.8020 (t0) cc_final: 0.7661 (m-40) REVERT: A 654 GLU cc_start: 0.7772 (tt0) cc_final: 0.7440 (tm-30) REVERT: A 661 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7641 (mm-30) REVERT: A 779 GLN cc_start: 0.7791 (tp40) cc_final: 0.7344 (tt0) REVERT: A 814 LYS cc_start: 0.7478 (mttp) cc_final: 0.7168 (mtpt) REVERT: A 854 LYS cc_start: 0.4439 (mttp) cc_final: 0.3704 (ptpt) REVERT: A 988 GLU cc_start: 0.7049 (tp30) cc_final: 0.6625 (mp0) REVERT: A 1092 GLU cc_start: 0.7025 (mp0) cc_final: 0.6711 (mt-10) REVERT: A 1128 VAL cc_start: 0.8444 (t) cc_final: 0.8103 (p) REVERT: B 52 GLN cc_start: 0.8363 (tt0) cc_final: 0.8062 (tp40) REVERT: B 231 ILE cc_start: 0.7913 (pt) cc_final: 0.7662 (pp) REVERT: B 271 GLN cc_start: 0.7952 (mt0) cc_final: 0.7133 (mp10) REVERT: B 564 GLN cc_start: 0.6822 (OUTLIER) cc_final: 0.5850 (mm-40) REVERT: B 568 ASP cc_start: 0.7570 (t0) cc_final: 0.7323 (m-30) REVERT: B 569 ILE cc_start: 0.8007 (mm) cc_final: 0.7598 (tt) REVERT: B 572 THR cc_start: 0.7712 (t) cc_final: 0.7430 (t) REVERT: B 583 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7569 (pt0) REVERT: B 612 TYR cc_start: 0.8621 (m-80) cc_final: 0.8372 (m-80) REVERT: B 646 ARG cc_start: 0.7260 (ttm170) cc_final: 0.6428 (tpt90) REVERT: B 698 SER cc_start: 0.8407 (t) cc_final: 0.8077 (p) REVERT: B 814 LYS cc_start: 0.7339 (mttt) cc_final: 0.6651 (mmmt) REVERT: B 988 GLU cc_start: 0.7299 (tp30) cc_final: 0.6584 (mp0) REVERT: B 994 ASP cc_start: 0.7008 (OUTLIER) cc_final: 0.6497 (m-30) REVERT: B 998 THR cc_start: 0.8525 (m) cc_final: 0.8230 (m) REVERT: B 1010 GLN cc_start: 0.7340 (mm-40) cc_final: 0.6751 (pt0) REVERT: B 1045 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7576 (mptt) REVERT: B 1113 GLN cc_start: 0.7881 (mt0) cc_final: 0.7284 (mt0) REVERT: B 1118 ASP cc_start: 0.7905 (m-30) cc_final: 0.7494 (t0) REVERT: C 84 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6273 (mt) REVERT: C 287 ASP cc_start: 0.7834 (m-30) cc_final: 0.7447 (m-30) REVERT: C 317 ASN cc_start: 0.8023 (t0) cc_final: 0.7650 (t0) REVERT: C 378 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7498 (mtmt) REVERT: C 396 TYR cc_start: 0.7329 (m-80) cc_final: 0.6853 (m-80) REVERT: C 424 LYS cc_start: 0.6484 (tptp) cc_final: 0.5981 (tptp) REVERT: C 516 GLU cc_start: 0.7749 (tp30) cc_final: 0.7448 (tp30) REVERT: C 528 LYS cc_start: 0.7161 (tttt) cc_final: 0.6523 (tppt) REVERT: C 564 GLN cc_start: 0.7140 (tp40) cc_final: 0.6864 (mp-120) REVERT: C 643 PHE cc_start: 0.6173 (t80) cc_final: 0.5793 (t80) REVERT: C 675 GLN cc_start: 0.7367 (mt0) cc_final: 0.7014 (mt0) REVERT: C 786 LYS cc_start: 0.6921 (pttt) cc_final: 0.6600 (pttt) REVERT: C 790 LYS cc_start: 0.8265 (pttt) cc_final: 0.7438 (mtpt) REVERT: C 814 LYS cc_start: 0.7487 (mttt) cc_final: 0.6948 (mtpt) REVERT: C 990 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6528 (mp0) REVERT: C 994 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7342 (m-30) REVERT: C 995 ARG cc_start: 0.7529 (mtt180) cc_final: 0.6993 (mtp180) REVERT: C 1010 GLN cc_start: 0.7528 (mm-40) cc_final: 0.6937 (pt0) REVERT: C 1136 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8655 (t) REVERT: C 1145 LEU cc_start: 0.4076 (OUTLIER) cc_final: 0.3467 (pp) outliers start: 48 outliers final: 32 residues processed: 248 average time/residue: 1.2627 time to fit residues: 384.5031 Evaluate side-chains 260 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 CYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 141 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 chunk 232 optimal weight: 0.1980 chunk 142 optimal weight: 0.7980 chunk 235 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 259 optimal weight: 0.0570 chunk 152 optimal weight: 4.9990 chunk 254 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN C 334 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.218416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.156742 restraints weight = 22309.793| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.86 r_work: 0.3671 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 23364 Z= 0.101 Angle : 0.494 9.769 31818 Z= 0.257 Chirality : 0.044 0.176 3633 Planarity : 0.004 0.044 4107 Dihedral : 4.148 30.480 3099 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.64 % Allowed : 13.76 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 2844 helix: 2.08 (0.20), residues: 681 sheet: -0.06 (0.20), residues: 628 loop : -0.51 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A1088 PHE 0.028 0.001 PHE B 168 TYR 0.022 0.001 TYR B 170 ARG 0.003 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 1021) hydrogen bonds : angle 5.22591 ( 2826) SS BOND : bond 0.00352 ( 39) SS BOND : angle 1.91504 ( 78) covalent geometry : bond 0.00229 (23325) covalent geometry : angle 0.48534 (31740) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 2.647 Fit side-chains REVERT: A 47 VAL cc_start: 0.7754 (t) cc_final: 0.7512 (p) REVERT: A 200 TYR cc_start: 0.6960 (OUTLIER) cc_final: 0.5976 (t80) REVERT: A 239 GLN cc_start: 0.7407 (tt0) cc_final: 0.6890 (tt0) REVERT: A 351 TYR cc_start: 0.5298 (p90) cc_final: 0.4562 (p90) REVERT: A 378 LYS cc_start: 0.7257 (tptp) cc_final: 0.6906 (pttm) REVERT: A 532 ASN cc_start: 0.8015 (t0) cc_final: 0.7679 (m-40) REVERT: A 654 GLU cc_start: 0.7789 (tt0) cc_final: 0.7452 (tm-30) REVERT: A 661 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7642 (mm-30) REVERT: A 779 GLN cc_start: 0.7722 (tp40) cc_final: 0.7313 (tt0) REVERT: A 814 LYS cc_start: 0.7528 (mttp) cc_final: 0.7214 (mtpt) REVERT: A 854 LYS cc_start: 0.4497 (mttp) cc_final: 0.3754 (ptpt) REVERT: A 988 GLU cc_start: 0.7038 (tp30) cc_final: 0.6625 (mp0) REVERT: A 995 ARG cc_start: 0.7430 (mtt180) cc_final: 0.6840 (mtp180) REVERT: A 1092 GLU cc_start: 0.6953 (mp0) cc_final: 0.6609 (mt-10) REVERT: A 1128 VAL cc_start: 0.8409 (t) cc_final: 0.8092 (p) REVERT: B 52 GLN cc_start: 0.8332 (tt0) cc_final: 0.8042 (tp40) REVERT: B 170 TYR cc_start: 0.6667 (t80) cc_final: 0.6391 (t80) REVERT: B 271 GLN cc_start: 0.7906 (mt0) cc_final: 0.7115 (mp10) REVERT: B 564 GLN cc_start: 0.6818 (OUTLIER) cc_final: 0.5853 (mm-40) REVERT: B 568 ASP cc_start: 0.7452 (t0) cc_final: 0.7196 (m-30) REVERT: B 572 THR cc_start: 0.7712 (t) cc_final: 0.7443 (t) REVERT: B 583 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: B 612 TYR cc_start: 0.8630 (m-80) cc_final: 0.8357 (m-80) REVERT: B 646 ARG cc_start: 0.7275 (ttm170) cc_final: 0.6437 (tpt90) REVERT: B 698 SER cc_start: 0.8310 (t) cc_final: 0.7980 (p) REVERT: B 779 GLN cc_start: 0.7461 (tp40) cc_final: 0.7255 (tt0) REVERT: B 814 LYS cc_start: 0.7313 (mttt) cc_final: 0.6667 (mmmt) REVERT: B 988 GLU cc_start: 0.7335 (tp30) cc_final: 0.6654 (mp0) REVERT: B 994 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.6628 (m-30) REVERT: B 998 THR cc_start: 0.8483 (m) cc_final: 0.8203 (m) REVERT: B 1010 GLN cc_start: 0.7322 (mm-40) cc_final: 0.6783 (pt0) REVERT: B 1045 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7591 (mptp) REVERT: B 1113 GLN cc_start: 0.7890 (mt0) cc_final: 0.7339 (mt0) REVERT: B 1118 ASP cc_start: 0.7878 (m-30) cc_final: 0.7478 (t0) REVERT: C 84 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6280 (mt) REVERT: C 287 ASP cc_start: 0.7861 (m-30) cc_final: 0.7443 (m-30) REVERT: C 317 ASN cc_start: 0.7988 (t0) cc_final: 0.7601 (t0) REVERT: C 378 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7475 (ttmt) REVERT: C 396 TYR cc_start: 0.7296 (m-80) cc_final: 0.6833 (m-80) REVERT: C 424 LYS cc_start: 0.6499 (tptp) cc_final: 0.6018 (tptp) REVERT: C 516 GLU cc_start: 0.7742 (tp30) cc_final: 0.7475 (tp30) REVERT: C 528 LYS cc_start: 0.7178 (tttt) cc_final: 0.6554 (tppt) REVERT: C 564 GLN cc_start: 0.7098 (tp40) cc_final: 0.6832 (mp-120) REVERT: C 643 PHE cc_start: 0.5948 (t80) cc_final: 0.5406 (t80) REVERT: C 675 GLN cc_start: 0.7371 (mt0) cc_final: 0.7003 (mt0) REVERT: C 786 LYS cc_start: 0.7026 (pttt) cc_final: 0.6678 (pttt) REVERT: C 790 LYS cc_start: 0.8233 (pttt) cc_final: 0.7452 (mtpt) REVERT: C 814 LYS cc_start: 0.7469 (mttt) cc_final: 0.6966 (mtpt) REVERT: C 990 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6545 (mp0) REVERT: C 994 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: C 995 ARG cc_start: 0.7494 (mtt180) cc_final: 0.7006 (mtp180) REVERT: C 1010 GLN cc_start: 0.7536 (mm-40) cc_final: 0.6990 (pt0) REVERT: C 1136 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8658 (t) REVERT: C 1145 LEU cc_start: 0.4210 (OUTLIER) cc_final: 0.3632 (pp) outliers start: 42 outliers final: 28 residues processed: 272 average time/residue: 0.9495 time to fit residues: 312.7543 Evaluate side-chains 271 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 CYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 168 optimal weight: 0.0970 chunk 90 optimal weight: 2.9990 chunk 255 optimal weight: 0.5980 chunk 150 optimal weight: 3.9990 chunk 285 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 262 optimal weight: 0.2980 chunk 97 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN C 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.216963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.157660 restraints weight = 22309.090| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.85 r_work: 0.3729 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23364 Z= 0.119 Angle : 0.511 10.313 31818 Z= 0.264 Chirality : 0.044 0.179 3633 Planarity : 0.004 0.045 4107 Dihedral : 4.168 30.435 3099 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.56 % Allowed : 14.15 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 2844 helix: 2.03 (0.20), residues: 682 sheet: -0.06 (0.20), residues: 626 loop : -0.47 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.003 0.001 HIS B1088 PHE 0.025 0.001 PHE B 168 TYR 0.020 0.001 TYR B 170 ARG 0.002 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 1021) hydrogen bonds : angle 5.26718 ( 2826) SS BOND : bond 0.00322 ( 39) SS BOND : angle 1.92216 ( 78) covalent geometry : bond 0.00280 (23325) covalent geometry : angle 0.50236 (31740) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18162.00 seconds wall clock time: 316 minutes 33.13 seconds (18993.13 seconds total)