Starting phenix.real_space_refine on Sun Sep 29 17:39:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tld_25988/09_2024/7tld_25988.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tld_25988/09_2024/7tld_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tld_25988/09_2024/7tld_25988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tld_25988/09_2024/7tld_25988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tld_25988/09_2024/7tld_25988.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tld_25988/09_2024/7tld_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 13.30, per 1000 atoms: 0.58 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: 5.40 Conformation dependent library (CDL) restraints added in 2.8 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: 3.50 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: 10.41 Time building geometry restraints manager: 6.39 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: 0.00 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 53.280 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.100 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:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.430 ------------------------------------------------------------------------------- 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 23325 Z= 0.812 Angle : 1.803 10.763 31740 Z= 1.231 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 *********************** 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 fitting. rotamer outliers: 24 poor density : 372 time to evaluate : 2.466 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: 1.0579 time to fit residues: 489.5927 Evaluate side-chains 275 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 268 time to evaluate : 2.582 ------------------------------------------------------------------------------- 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: 2.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4504 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 23325 Z= 0.198 Angle : 0.622 9.509 31740 Z= 0.334 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 *********************** 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 fitting. rotamer outliers: 42 poor density : 306 time to evaluate : 2.704 Fit side-chains REVERT: A 239 GLN cc_start: 0.5302 (tt0) cc_final: 0.4917 (tt0) REVERT: A 305 SER cc_start: 0.7183 (t) cc_final: 0.6694 (p) REVERT: A 307 THR cc_start: 0.6944 (m) cc_final: 0.6493 (p) REVERT: A 314 GLN cc_start: 0.5906 (tt0) cc_final: 0.5262 (tp-100) REVERT: A 321 GLN cc_start: 0.5679 (mm-40) cc_final: 0.5476 (mp10) REVERT: A 558 LYS cc_start: 0.7009 (tttt) cc_final: 0.6469 (mptp) REVERT: A 656 VAL cc_start: 0.5356 (t) cc_final: 0.5109 (m) REVERT: A 661 GLU cc_start: 0.6813 (mt-10) cc_final: 0.5845 (mm-30) REVERT: A 674 TYR cc_start: 0.7279 (t80) cc_final: 0.6793 (t80) REVERT: A 702 GLU cc_start: 0.7261 (tt0) cc_final: 0.6672 (tp30) REVERT: A 779 GLN cc_start: 0.4897 (tp40) cc_final: 0.4496 (tp40) REVERT: A 814 LYS cc_start: 0.6102 (mttp) cc_final: 0.5724 (mtpp) REVERT: A 854 LYS cc_start: 0.2397 (mttp) cc_final: 0.1881 (ptmt) REVERT: A 988 GLU cc_start: 0.5071 (tp30) cc_final: 0.4418 (mp0) REVERT: A 1010 GLN cc_start: 0.4464 (mt0) cc_final: 0.4038 (mm-40) REVERT: A 1092 GLU cc_start: 0.5264 (mp0) cc_final: 0.5024 (mt-10) REVERT: A 1107 ARG cc_start: 0.6547 (mtm180) cc_final: 0.5656 (mtt180) REVERT: B 271 GLN cc_start: 0.4641 (mt0) cc_final: 0.4170 (mp10) REVERT: B 314 GLN cc_start: 0.6980 (tt0) cc_final: 0.6274 (tp40) REVERT: B 317 ASN cc_start: 0.7275 (m-40) cc_final: 0.6861 (m110) REVERT: B 319 ARG cc_start: 0.5860 (mtm180) cc_final: 0.5606 (ttm110) REVERT: B 388 ASN cc_start: 0.6198 (m110) cc_final: 0.5923 (m-40) REVERT: B 389 ASP cc_start: 0.5820 (t0) cc_final: 0.5498 (m-30) REVERT: B 569 ILE cc_start: 0.6157 (mm) cc_final: 0.5863 (tt) REVERT: B 612 TYR cc_start: 0.5713 (m-80) cc_final: 0.5510 (m-80) REVERT: B 613 GLN cc_start: 0.6605 (mt0) cc_final: 0.6293 (mt0) REVERT: B 646 ARG cc_start: 0.6323 (ttm170) cc_final: 0.5240 (tpt170) REVERT: B 661 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6743 (mt-10) REVERT: B 697 MET cc_start: 0.6838 (ptm) cc_final: 0.6456 (ptp) REVERT: B 702 GLU cc_start: 0.7095 (tt0) cc_final: 0.6800 (tp30) REVERT: B 735 SER cc_start: 0.6480 (t) cc_final: 0.5962 (p) REVERT: B 790 LYS cc_start: 0.6686 (pttt) cc_final: 0.5925 (ptmm) REVERT: B 814 LYS cc_start: 0.6455 (mttt) cc_final: 0.5453 (mmmt) REVERT: B 988 GLU cc_start: 0.4902 (tp30) cc_final: 0.4306 (mp0) REVERT: B 1010 GLN cc_start: 0.4630 (mm-40) cc_final: 0.3761 (tt0) REVERT: B 1045 LYS cc_start: 0.6740 (ttpp) cc_final: 0.5984 (mptt) REVERT: B 1113 GLN cc_start: 0.5959 (mt0) cc_final: 0.4977 (mt0) REVERT: B 1119 ASN cc_start: 0.5438 (m-40) cc_final: 0.4732 (m110) REVERT: C 273 ARG cc_start: 0.3722 (mmt90) cc_final: 0.3341 (mmt-90) REVERT: C 305 SER cc_start: 0.6647 (t) cc_final: 0.6097 (p) REVERT: C 340 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7051 (mp0) REVERT: C 383 CYS cc_start: 0.5064 (t) cc_final: 0.4621 (t) REVERT: C 396 TYR cc_start: 0.4342 (m-80) cc_final: 0.3326 (m-80) REVERT: C 424 LYS cc_start: 0.4156 (tptp) cc_final: 0.3743 (tptt) REVERT: C 528 LYS cc_start: 0.6049 (tttt) cc_final: 0.5284 (ttmm) REVERT: C 567 ARG cc_start: 0.4721 (mtt-85) cc_final: 0.4375 (mmm-85) REVERT: C 661 GLU cc_start: 0.5869 (mm-30) cc_final: 0.5647 (tp30) REVERT: C 675 GLN cc_start: 0.5259 (mt0) cc_final: 0.4952 (mt0) REVERT: C 702 GLU cc_start: 0.7466 (tt0) cc_final: 0.6908 (tp30) REVERT: C 776 LYS cc_start: 0.5346 (tttt) cc_final: 0.5092 (ttmp) REVERT: C 814 LYS cc_start: 0.5954 (mttt) cc_final: 0.5323 (mtpt) REVERT: C 823 PHE cc_start: 0.6145 (m-80) cc_final: 0.5893 (m-80) REVERT: C 907 ASN cc_start: 0.6389 (OUTLIER) cc_final: 0.6158 (m-40) REVERT: C 990 GLU cc_start: 0.3823 (mt-10) cc_final: 0.3232 (mp0) REVERT: C 1010 GLN cc_start: 0.5190 (mm-40) cc_final: 0.4427 (tt0) outliers start: 42 outliers final: 16 residues processed: 333 average time/residue: 0.9606 time to fit residues: 385.2842 Evaluate side-chains 259 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 242 time to evaluate : 2.500 ------------------------------------------------------------------------------- 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 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 907 ASN 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 146 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 285 optimal weight: 0.0980 chunk 235 optimal weight: 10.0000 chunk 262 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 212 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 B 334 ASN B 394 ASN B 907 ASN C 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4541 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23325 Z= 0.281 Angle : 0.602 10.652 31740 Z= 0.318 Chirality : 0.047 0.179 3633 Planarity : 0.004 0.039 4107 Dihedral : 5.294 48.267 3104 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.65 % Allowed : 8.46 % Favored : 88.89 % 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: 1.41 (0.20), residues: 679 sheet: -0.34 (0.19), residues: 677 loop : -0.63 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 64 HIS 0.005 0.001 HIS A1088 PHE 0.027 0.002 PHE B 168 TYR 0.022 0.002 TYR B1067 ARG 0.010 0.001 ARG C 237 *********************** 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 336 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 268 time to evaluate : 2.515 Fit side-chains REVERT: A 47 VAL cc_start: 0.5750 (OUTLIER) cc_final: 0.5450 (p) REVERT: A 228 ASP cc_start: 0.4445 (t0) cc_final: 0.3973 (t0) REVERT: A 239 GLN cc_start: 0.5430 (tt0) cc_final: 0.5088 (tt0) REVERT: A 305 SER cc_start: 0.7212 (t) cc_final: 0.6778 (p) REVERT: A 314 GLN cc_start: 0.6076 (tt0) cc_final: 0.5453 (tp-100) REVERT: A 321 GLN cc_start: 0.5992 (mm-40) cc_final: 0.5735 (mp10) REVERT: A 378 LYS cc_start: 0.4401 (pttm) cc_final: 0.4168 (pttm) REVERT: A 558 LYS cc_start: 0.7057 (tttt) cc_final: 0.6507 (mptp) REVERT: A 578 ASP cc_start: 0.5199 (t0) cc_final: 0.4861 (t0) REVERT: A 603 ASN cc_start: 0.6829 (t0) cc_final: 0.6377 (m-40) REVERT: A 616 ASN cc_start: 0.3584 (m-40) cc_final: 0.3317 (m-40) REVERT: A 661 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6052 (mm-30) REVERT: A 674 TYR cc_start: 0.7472 (t80) cc_final: 0.7074 (t80) REVERT: A 702 GLU cc_start: 0.7319 (tt0) cc_final: 0.6760 (tp30) REVERT: A 779 GLN cc_start: 0.4907 (tp40) cc_final: 0.4488 (tp40) REVERT: A 814 LYS cc_start: 0.6218 (mttp) cc_final: 0.5795 (mtpp) REVERT: A 854 LYS cc_start: 0.2533 (mttp) cc_final: 0.2068 (ptpt) REVERT: A 988 GLU cc_start: 0.4915 (tp30) cc_final: 0.4394 (mp0) REVERT: A 1010 GLN cc_start: 0.4393 (mt0) cc_final: 0.4085 (mm-40) REVERT: A 1092 GLU cc_start: 0.5479 (mp0) cc_final: 0.5210 (mt-10) REVERT: A 1107 ARG cc_start: 0.6657 (mtm180) cc_final: 0.5734 (mtt180) REVERT: A 1128 VAL cc_start: 0.7413 (t) cc_final: 0.7042 (p) REVERT: B 271 GLN cc_start: 0.4330 (mt0) cc_final: 0.3858 (mp10) REVERT: B 314 GLN cc_start: 0.7254 (tt0) cc_final: 0.6636 (tp40) REVERT: B 317 ASN cc_start: 0.7351 (m-40) cc_final: 0.6982 (m110) REVERT: B 319 ARG cc_start: 0.6016 (mtm180) cc_final: 0.5786 (ttm110) REVERT: B 528 LYS cc_start: 0.6837 (tttt) cc_final: 0.6523 (ttmt) REVERT: B 534 VAL cc_start: 0.7268 (t) cc_final: 0.6849 (m) REVERT: B 564 GLN cc_start: 0.4370 (OUTLIER) cc_final: 0.3677 (mm-40) REVERT: B 569 ILE cc_start: 0.6273 (mm) cc_final: 0.5930 (tt) REVERT: B 612 TYR cc_start: 0.6005 (m-80) cc_final: 0.5720 (m-80) REVERT: B 613 GLN cc_start: 0.6808 (mt0) cc_final: 0.6410 (mt0) REVERT: B 646 ARG cc_start: 0.6329 (ttm170) cc_final: 0.5229 (tpt170) REVERT: B 661 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6734 (mt-10) REVERT: B 702 GLU cc_start: 0.7076 (tt0) cc_final: 0.6796 (tp30) REVERT: B 735 SER cc_start: 0.6918 (t) cc_final: 0.6150 (p) REVERT: B 762 GLN cc_start: 0.5463 (pt0) cc_final: 0.5198 (pt0) REVERT: B 790 LYS cc_start: 0.6648 (pttt) cc_final: 0.6171 (ptmm) REVERT: B 814 LYS cc_start: 0.6488 (mttt) cc_final: 0.5484 (mmmt) REVERT: B 988 GLU cc_start: 0.4903 (tp30) cc_final: 0.4366 (mp0) REVERT: B 1010 GLN cc_start: 0.4762 (mm-40) cc_final: 0.3795 (pt0) REVERT: B 1045 LYS cc_start: 0.6765 (ttpp) cc_final: 0.5963 (mptp) REVERT: B 1113 GLN cc_start: 0.5931 (mt0) cc_final: 0.4848 (mt0) REVERT: B 1119 ASN cc_start: 0.5516 (m-40) cc_final: 0.5304 (m-40) REVERT: C 84 LEU cc_start: 0.3296 (OUTLIER) cc_final: 0.2950 (mt) REVERT: C 273 ARG cc_start: 0.3840 (mmt90) cc_final: 0.3524 (mmt-90) REVERT: C 305 SER cc_start: 0.6715 (t) cc_final: 0.6201 (p) REVERT: C 340 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7056 (mp0) REVERT: C 359 SER cc_start: 0.6969 (p) cc_final: 0.6628 (m) REVERT: C 383 CYS cc_start: 0.5230 (t) cc_final: 0.4869 (t) REVERT: C 392 PHE cc_start: 0.4106 (m-80) cc_final: 0.3904 (m-80) REVERT: C 394 ASN cc_start: 0.5989 (OUTLIER) cc_final: 0.4965 (p0) REVERT: C 396 TYR cc_start: 0.4899 (m-80) cc_final: 0.4319 (m-80) REVERT: C 424 LYS cc_start: 0.4172 (tptp) cc_final: 0.3830 (tptp) REVERT: C 516 GLU cc_start: 0.5252 (tp30) cc_final: 0.4815 (mt-10) REVERT: C 528 LYS cc_start: 0.5824 (tttt) cc_final: 0.5184 (tppt) REVERT: C 574 ASP cc_start: 0.5910 (t0) cc_final: 0.5659 (t0) REVERT: C 675 GLN cc_start: 0.5358 (mt0) cc_final: 0.4844 (mt0) REVERT: C 702 GLU cc_start: 0.7731 (tt0) cc_final: 0.7213 (tp30) REVERT: C 704 SER cc_start: 0.7475 (p) cc_final: 0.7139 (t) REVERT: C 776 LYS cc_start: 0.5326 (tttt) cc_final: 0.5069 (ttmp) REVERT: C 814 LYS cc_start: 0.5789 (mttt) cc_final: 0.5126 (mtpt) REVERT: C 990 GLU cc_start: 0.3771 (mt-10) cc_final: 0.3294 (mp0) REVERT: C 1010 GLN cc_start: 0.5158 (mm-40) cc_final: 0.4379 (tt0) outliers start: 68 outliers final: 31 residues processed: 313 average time/residue: 0.9840 time to fit residues: 369.8152 Evaluate side-chains 274 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 239 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 510 VAL 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 704 SER 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 564 GLN 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 B residue 985 CYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 791 THR 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 261 optimal weight: 0.0570 chunk 199 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 281 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 chunk 251 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- 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 969 ASN B 394 ASN B 641 ASN B 957 GLN C 196 ASN C 907 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4531 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23325 Z= 0.205 Angle : 0.535 6.888 31740 Z= 0.284 Chirality : 0.045 0.166 3633 Planarity : 0.004 0.038 4107 Dihedral : 4.885 34.718 3102 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.22 % Allowed : 10.53 % Favored : 87.25 % 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: 1.68 (0.20), residues: 679 sheet: -0.28 (0.19), residues: 642 loop : -0.59 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.003 0.001 HIS A1088 PHE 0.030 0.001 PHE B 168 TYR 0.024 0.001 TYR B 170 ARG 0.003 0.000 ARG C 237 *********************** 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 318 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 261 time to evaluate : 2.750 Fit side-chains revert: symmetry clash REVERT: A 47 VAL cc_start: 0.5883 (t) cc_final: 0.5587 (p) REVERT: A 200 TYR cc_start: 0.4411 (OUTLIER) cc_final: 0.4207 (t80) REVERT: A 239 GLN cc_start: 0.5447 (tt0) cc_final: 0.5108 (tt0) REVERT: A 305 SER cc_start: 0.7291 (t) cc_final: 0.6883 (p) REVERT: A 314 GLN cc_start: 0.6297 (tt0) cc_final: 0.5651 (tp-100) REVERT: A 378 LYS cc_start: 0.4536 (pttm) cc_final: 0.4313 (pttm) REVERT: A 558 LYS cc_start: 0.7053 (tttt) cc_final: 0.6482 (mptp) REVERT: A 661 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6114 (mm-30) REVERT: A 674 TYR cc_start: 0.7472 (t80) cc_final: 0.7092 (t80) REVERT: A 702 GLU cc_start: 0.7305 (tt0) cc_final: 0.6747 (tp30) REVERT: A 779 GLN cc_start: 0.4888 (tp40) cc_final: 0.4470 (tp40) REVERT: A 814 LYS cc_start: 0.6422 (mttp) cc_final: 0.5986 (mtpp) REVERT: A 854 LYS cc_start: 0.2422 (mttp) cc_final: 0.2002 (ptpt) REVERT: A 988 GLU cc_start: 0.5064 (tp30) cc_final: 0.4526 (mp0) REVERT: A 1010 GLN cc_start: 0.4551 (mt0) cc_final: 0.4217 (mm-40) REVERT: A 1092 GLU cc_start: 0.5502 (mp0) cc_final: 0.5274 (mt-10) REVERT: A 1107 ARG cc_start: 0.6458 (mtm180) cc_final: 0.5556 (mtt180) REVERT: A 1128 VAL cc_start: 0.7586 (t) cc_final: 0.7195 (p) REVERT: B 271 GLN cc_start: 0.4417 (mt0) cc_final: 0.3941 (mp10) REVERT: B 314 GLN cc_start: 0.7226 (tt0) cc_final: 0.6477 (tp40) REVERT: B 317 ASN cc_start: 0.7367 (m-40) cc_final: 0.7000 (m110) REVERT: B 319 ARG cc_start: 0.5983 (mtm180) cc_final: 0.5768 (ttm110) REVERT: B 324 GLU cc_start: 0.4040 (pt0) cc_final: 0.3480 (pm20) REVERT: B 534 VAL cc_start: 0.7312 (t) cc_final: 0.6765 (m) REVERT: B 564 GLN cc_start: 0.4390 (OUTLIER) cc_final: 0.3691 (mm-40) REVERT: B 569 ILE cc_start: 0.6260 (mm) cc_final: 0.5935 (tt) REVERT: B 613 GLN cc_start: 0.6869 (mt0) cc_final: 0.6569 (mt0) REVERT: B 646 ARG cc_start: 0.6333 (ttm170) cc_final: 0.5238 (tpt170) REVERT: B 661 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6755 (mt-10) REVERT: B 698 SER cc_start: 0.6955 (t) cc_final: 0.6368 (p) REVERT: B 702 GLU cc_start: 0.7031 (tt0) cc_final: 0.6776 (tp30) REVERT: B 735 SER cc_start: 0.6886 (t) cc_final: 0.6117 (p) REVERT: B 790 LYS cc_start: 0.6704 (pttt) cc_final: 0.6265 (ptmm) REVERT: B 814 LYS cc_start: 0.6500 (mttt) cc_final: 0.5433 (mmmt) REVERT: B 988 GLU cc_start: 0.4885 (tp30) cc_final: 0.4348 (mp0) REVERT: B 1010 GLN cc_start: 0.4831 (mm-40) cc_final: 0.3860 (pt0) REVERT: B 1045 LYS cc_start: 0.6721 (ttpp) cc_final: 0.5936 (mptt) REVERT: B 1113 GLN cc_start: 0.5969 (mt0) cc_final: 0.4874 (mt0) REVERT: B 1119 ASN cc_start: 0.5601 (m-40) cc_final: 0.5385 (m-40) REVERT: C 305 SER cc_start: 0.6879 (t) cc_final: 0.6398 (p) REVERT: C 317 ASN cc_start: 0.7304 (t0) cc_final: 0.7012 (t0) REVERT: C 340 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7035 (mp0) REVERT: C 378 LYS cc_start: 0.5899 (OUTLIER) cc_final: 0.5482 (ttmt) REVERT: C 383 CYS cc_start: 0.5143 (t) cc_final: 0.4836 (t) REVERT: C 396 TYR cc_start: 0.4861 (m-80) cc_final: 0.4437 (m-80) REVERT: C 424 LYS cc_start: 0.4326 (tptp) cc_final: 0.3965 (tptp) REVERT: C 528 LYS cc_start: 0.5989 (tttt) cc_final: 0.5301 (tppt) REVERT: C 675 GLN cc_start: 0.5335 (mt0) cc_final: 0.4825 (mt0) REVERT: C 702 GLU cc_start: 0.7738 (tt0) cc_final: 0.7175 (tp30) REVERT: C 704 SER cc_start: 0.7475 (p) cc_final: 0.7067 (t) REVERT: C 776 LYS cc_start: 0.5306 (tttt) cc_final: 0.5030 (ttmp) REVERT: C 814 LYS cc_start: 0.5977 (mttt) cc_final: 0.5234 (mtpt) REVERT: C 950 ASP cc_start: 0.5793 (m-30) cc_final: 0.5554 (m-30) REVERT: C 990 GLU cc_start: 0.3736 (mt-10) cc_final: 0.3257 (mp0) REVERT: C 1010 GLN cc_start: 0.5172 (mm-40) cc_final: 0.4388 (tt0) outliers start: 57 outliers final: 33 residues processed: 303 average time/residue: 0.9149 time to fit residues: 336.5064 Evaluate side-chains 277 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 241 time to evaluate : 2.477 ------------------------------------------------------------------------------- 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 510 VAL 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 791 THR 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 564 GLN 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 B residue 985 CYS Chi-restraints excluded: chain B residue 1128 VAL 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 859 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 209 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 240 optimal weight: 0.6980 chunk 194 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 252 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 A 914 ASN A 935 GLN B 30 ASN B 394 ASN C 907 ASN C1088 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4550 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23325 Z= 0.315 Angle : 0.577 7.355 31740 Z= 0.303 Chirality : 0.047 0.172 3633 Planarity : 0.004 0.042 4107 Dihedral : 4.958 38.285 3102 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.92 % Allowed : 10.68 % Favored : 86.39 % 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: -0.16 (0.15), residues: 2844 helix: 1.59 (0.20), residues: 674 sheet: -0.45 (0.19), residues: 642 loop : -0.70 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.005 0.001 HIS C1048 PHE 0.020 0.002 PHE B 168 TYR 0.023 0.002 TYR B1067 ARG 0.009 0.000 ARG C 237 *********************** 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 317 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 242 time to evaluate : 2.935 Fit side-chains REVERT: A 47 VAL cc_start: 0.5852 (t) cc_final: 0.5547 (p) REVERT: A 88 ASP cc_start: 0.6583 (OUTLIER) cc_final: 0.5899 (t0) REVERT: A 239 GLN cc_start: 0.5362 (tt0) cc_final: 0.5017 (tt0) REVERT: A 305 SER cc_start: 0.7200 (t) cc_final: 0.6817 (p) REVERT: A 314 GLN cc_start: 0.6335 (tt0) cc_final: 0.5713 (tp-100) REVERT: A 321 GLN cc_start: 0.6151 (mm-40) cc_final: 0.5924 (mp-120) REVERT: A 378 LYS cc_start: 0.4477 (pttm) cc_final: 0.4256 (pttm) REVERT: A 558 LYS cc_start: 0.7045 (tttt) cc_final: 0.6452 (mptp) REVERT: A 603 ASN cc_start: 0.6738 (t0) cc_final: 0.6351 (m110) REVERT: A 661 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6127 (mm-30) REVERT: A 702 GLU cc_start: 0.7298 (tt0) cc_final: 0.6742 (tp30) REVERT: A 779 GLN cc_start: 0.4844 (tp40) cc_final: 0.4432 (tp40) REVERT: A 814 LYS cc_start: 0.6353 (mttp) cc_final: 0.5864 (mtpt) REVERT: A 854 LYS cc_start: 0.2410 (mttp) cc_final: 0.1965 (ptpt) REVERT: A 969 ASN cc_start: 0.5864 (OUTLIER) cc_final: 0.5475 (m-40) REVERT: A 988 GLU cc_start: 0.4858 (tp30) cc_final: 0.4448 (mp0) REVERT: A 1010 GLN cc_start: 0.4608 (mt0) cc_final: 0.4278 (mm-40) REVERT: A 1092 GLU cc_start: 0.5562 (mp0) cc_final: 0.5245 (mt-10) REVERT: A 1107 ARG cc_start: 0.6688 (mtm180) cc_final: 0.5696 (mtt180) REVERT: A 1128 VAL cc_start: 0.7556 (t) cc_final: 0.7144 (p) REVERT: B 271 GLN cc_start: 0.4334 (mt0) cc_final: 0.3840 (mp10) REVERT: B 314 GLN cc_start: 0.7288 (tt0) cc_final: 0.6531 (tp40) REVERT: B 319 ARG cc_start: 0.5988 (mtm180) cc_final: 0.5555 (ttm110) REVERT: B 324 GLU cc_start: 0.4014 (pt0) cc_final: 0.3379 (pm20) REVERT: B 383 CYS cc_start: 0.5301 (t) cc_final: 0.5099 (t) REVERT: B 534 VAL cc_start: 0.7461 (t) cc_final: 0.6876 (m) REVERT: B 564 GLN cc_start: 0.4408 (OUTLIER) cc_final: 0.3725 (mm-40) REVERT: B 569 ILE cc_start: 0.6143 (mm) cc_final: 0.5741 (tt) REVERT: B 574 ASP cc_start: 0.4945 (t0) cc_final: 0.4706 (t0) REVERT: B 613 GLN cc_start: 0.6746 (mt0) cc_final: 0.6440 (mt0) REVERT: B 646 ARG cc_start: 0.6349 (ttm170) cc_final: 0.5345 (tpt170) REVERT: B 661 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6760 (mt-10) REVERT: B 697 MET cc_start: 0.6907 (ptp) cc_final: 0.6633 (ptp) REVERT: B 698 SER cc_start: 0.6779 (t) cc_final: 0.6214 (p) REVERT: B 702 GLU cc_start: 0.7067 (tt0) cc_final: 0.6800 (tp30) REVERT: B 735 SER cc_start: 0.6851 (t) cc_final: 0.6477 (t) REVERT: B 790 LYS cc_start: 0.6727 (pttt) cc_final: 0.6282 (ptmm) REVERT: B 814 LYS cc_start: 0.6478 (mttt) cc_final: 0.5389 (mmmt) REVERT: B 912 THR cc_start: 0.6764 (OUTLIER) cc_final: 0.6428 (p) REVERT: B 988 GLU cc_start: 0.4903 (tp30) cc_final: 0.4393 (mp0) REVERT: B 1010 GLN cc_start: 0.4832 (mm-40) cc_final: 0.3857 (pt0) REVERT: B 1045 LYS cc_start: 0.6708 (ttpp) cc_final: 0.5880 (mptp) REVERT: B 1113 GLN cc_start: 0.5796 (mt0) cc_final: 0.4750 (mt0) REVERT: C 305 SER cc_start: 0.6842 (t) cc_final: 0.6333 (p) REVERT: C 317 ASN cc_start: 0.7361 (t0) cc_final: 0.7077 (t0) REVERT: C 340 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7116 (mp0) REVERT: C 359 SER cc_start: 0.6761 (p) cc_final: 0.6339 (m) REVERT: C 378 LYS cc_start: 0.5905 (OUTLIER) cc_final: 0.5464 (mtmt) REVERT: C 383 CYS cc_start: 0.5152 (t) cc_final: 0.4868 (t) REVERT: C 396 TYR cc_start: 0.4723 (m-80) cc_final: 0.3887 (m-80) REVERT: C 424 LYS cc_start: 0.4218 (tptp) cc_final: 0.3960 (tptp) REVERT: C 516 GLU cc_start: 0.5543 (tp30) cc_final: 0.4561 (mt-10) REVERT: C 528 LYS cc_start: 0.5894 (tttt) cc_final: 0.5199 (tppt) REVERT: C 675 GLN cc_start: 0.5337 (mt0) cc_final: 0.4829 (mt0) REVERT: C 702 GLU cc_start: 0.7689 (tt0) cc_final: 0.7132 (tp30) REVERT: C 776 LYS cc_start: 0.5330 (tttt) cc_final: 0.5087 (ttmp) REVERT: C 814 LYS cc_start: 0.6039 (mttt) cc_final: 0.5280 (mtpt) REVERT: C 912 THR cc_start: 0.6574 (OUTLIER) cc_final: 0.6263 (p) REVERT: C 990 GLU cc_start: 0.3781 (mt-10) cc_final: 0.3299 (mp0) REVERT: C 1010 GLN cc_start: 0.5151 (mm-40) cc_final: 0.4229 (pt0) outliers start: 75 outliers final: 41 residues processed: 292 average time/residue: 0.9910 time to fit residues: 350.3793 Evaluate side-chains 277 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 230 time to evaluate : 2.546 ------------------------------------------------------------------------------- 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 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 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 266 TYR 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 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain B residue 1128 VAL 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 859 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1133 VAL 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 94 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 281 optimal weight: 0.8980 chunk 233 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 147 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 969 ASN B 394 ASN C 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4523 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 23325 Z= 0.158 Angle : 0.499 7.338 31740 Z= 0.263 Chirality : 0.044 0.165 3633 Planarity : 0.004 0.042 4107 Dihedral : 4.549 33.087 3102 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.22 % Allowed : 11.89 % Favored : 85.89 % 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: 2.06 (0.20), residues: 658 sheet: -0.33 (0.19), residues: 605 loop : -0.58 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.002 0.001 HIS A1088 PHE 0.029 0.001 PHE B 168 TYR 0.028 0.001 TYR B 170 ARG 0.007 0.000 ARG C 237 *********************** 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 316 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 259 time to evaluate : 2.421 Fit side-chains REVERT: A 47 VAL cc_start: 0.5524 (t) cc_final: 0.5194 (p) REVERT: A 228 ASP cc_start: 0.6512 (t0) cc_final: 0.6249 (t0) REVERT: A 239 GLN cc_start: 0.5402 (tt0) cc_final: 0.5046 (tt0) REVERT: A 305 SER cc_start: 0.7327 (t) cc_final: 0.6908 (p) REVERT: A 314 GLN cc_start: 0.6516 (tt0) cc_final: 0.5865 (tp-100) REVERT: A 321 GLN cc_start: 0.6225 (mm-40) cc_final: 0.5950 (mp-120) REVERT: A 378 LYS cc_start: 0.4507 (pttm) cc_final: 0.4287 (pttm) REVERT: A 558 LYS cc_start: 0.7056 (tttt) cc_final: 0.6395 (mptp) REVERT: A 578 ASP cc_start: 0.4538 (t0) cc_final: 0.3930 (t70) REVERT: A 661 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6107 (mm-30) REVERT: A 674 TYR cc_start: 0.7579 (t80) cc_final: 0.7159 (t80) REVERT: A 702 GLU cc_start: 0.7306 (tt0) cc_final: 0.6757 (tp30) REVERT: A 779 GLN cc_start: 0.4841 (tp40) cc_final: 0.4437 (tp40) REVERT: A 814 LYS cc_start: 0.6325 (mttp) cc_final: 0.5905 (mtpt) REVERT: A 854 LYS cc_start: 0.2454 (mttp) cc_final: 0.2033 (ptpt) REVERT: A 1010 GLN cc_start: 0.4526 (mt0) cc_final: 0.4252 (mm-40) REVERT: A 1092 GLU cc_start: 0.5469 (mp0) cc_final: 0.5230 (mt-10) REVERT: A 1107 ARG cc_start: 0.6576 (mtm180) cc_final: 0.5645 (mtt180) REVERT: A 1128 VAL cc_start: 0.7511 (t) cc_final: 0.7108 (p) REVERT: B 52 GLN cc_start: 0.7194 (tt0) cc_final: 0.6617 (tp40) REVERT: B 271 GLN cc_start: 0.4404 (mt0) cc_final: 0.3878 (mp10) REVERT: B 314 GLN cc_start: 0.7317 (tt0) cc_final: 0.6553 (tp40) REVERT: B 317 ASN cc_start: 0.7328 (m-40) cc_final: 0.6932 (m110) REVERT: B 319 ARG cc_start: 0.5832 (mtm180) cc_final: 0.5461 (ttm110) REVERT: B 324 GLU cc_start: 0.4122 (pt0) cc_final: 0.3579 (pm20) REVERT: B 534 VAL cc_start: 0.7519 (t) cc_final: 0.6984 (m) REVERT: B 568 ASP cc_start: 0.6203 (t0) cc_final: 0.5942 (m-30) REVERT: B 569 ILE cc_start: 0.6245 (mm) cc_final: 0.5953 (tt) REVERT: B 613 GLN cc_start: 0.6807 (mt0) cc_final: 0.6524 (mt0) REVERT: B 646 ARG cc_start: 0.6287 (ttm170) cc_final: 0.5262 (tpt170) REVERT: B 661 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6663 (mt-10) REVERT: B 697 MET cc_start: 0.6898 (ptp) cc_final: 0.6647 (ptp) REVERT: B 698 SER cc_start: 0.6786 (t) cc_final: 0.6273 (p) REVERT: B 702 GLU cc_start: 0.7031 (tt0) cc_final: 0.6549 (tp30) REVERT: B 735 SER cc_start: 0.6882 (t) cc_final: 0.6113 (p) REVERT: B 790 LYS cc_start: 0.6658 (pttt) cc_final: 0.6285 (ptmm) REVERT: B 814 LYS cc_start: 0.6514 (mttt) cc_final: 0.5400 (mmmt) REVERT: B 912 THR cc_start: 0.6729 (OUTLIER) cc_final: 0.6379 (p) REVERT: B 988 GLU cc_start: 0.4959 (tp30) cc_final: 0.4421 (mp0) REVERT: B 1010 GLN cc_start: 0.4855 (mm-40) cc_final: 0.3850 (pt0) REVERT: B 1045 LYS cc_start: 0.6774 (ttpp) cc_final: 0.5909 (mptt) REVERT: B 1074 ASN cc_start: 0.5648 (m-40) cc_final: 0.5343 (m-40) REVERT: B 1113 GLN cc_start: 0.5806 (mt0) cc_final: 0.4778 (mt0) REVERT: B 1119 ASN cc_start: 0.5201 (m-40) cc_final: 0.4969 (m110) REVERT: C 305 SER cc_start: 0.6881 (t) cc_final: 0.6408 (p) REVERT: C 317 ASN cc_start: 0.7401 (t0) cc_final: 0.7078 (t0) REVERT: C 359 SER cc_start: 0.6818 (p) cc_final: 0.6399 (m) REVERT: C 378 LYS cc_start: 0.6029 (OUTLIER) cc_final: 0.5565 (ttmt) REVERT: C 383 CYS cc_start: 0.5249 (t) cc_final: 0.4372 (t) REVERT: C 396 TYR cc_start: 0.4790 (m-80) cc_final: 0.4232 (m-80) REVERT: C 424 LYS cc_start: 0.4088 (tptp) cc_final: 0.3817 (tptp) REVERT: C 516 GLU cc_start: 0.5647 (tp30) cc_final: 0.5435 (tp30) REVERT: C 528 LYS cc_start: 0.5813 (tttt) cc_final: 0.5141 (tppt) REVERT: C 564 GLN cc_start: 0.5720 (tp40) cc_final: 0.5394 (mp-120) REVERT: C 569 ILE cc_start: 0.6547 (mm) cc_final: 0.6096 (tp) REVERT: C 675 GLN cc_start: 0.5315 (mt0) cc_final: 0.4767 (mt0) REVERT: C 702 GLU cc_start: 0.7665 (tt0) cc_final: 0.7075 (tp30) REVERT: C 704 SER cc_start: 0.7477 (p) cc_final: 0.7152 (t) REVERT: C 776 LYS cc_start: 0.5168 (tttt) cc_final: 0.4896 (ttmp) REVERT: C 790 LYS cc_start: 0.6386 (pttt) cc_final: 0.5611 (mttp) REVERT: C 814 LYS cc_start: 0.5941 (mttt) cc_final: 0.5171 (mtpt) REVERT: C 912 THR cc_start: 0.6857 (OUTLIER) cc_final: 0.6525 (p) REVERT: C 950 ASP cc_start: 0.5729 (m-30) cc_final: 0.5478 (m-30) REVERT: C 990 GLU cc_start: 0.3766 (mt-10) cc_final: 0.3284 (mp0) REVERT: C 995 ARG cc_start: 0.3958 (mtt180) cc_final: 0.3741 (mtp180) REVERT: C 1010 GLN cc_start: 0.5127 (mm-40) cc_final: 0.4128 (pt0) outliers start: 57 outliers final: 32 residues processed: 300 average time/residue: 0.9255 time to fit residues: 334.4036 Evaluate side-chains 274 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 239 time to evaluate : 2.515 ------------------------------------------------------------------------------- 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 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 649 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU 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 94 SER Chi-restraints excluded: chain B residue 266 TYR 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 615 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 985 CYS 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 912 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 159 optimal weight: 0.7980 chunk 237 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 280 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 394 ASN C 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4540 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23325 Z= 0.248 Angle : 0.528 7.978 31740 Z= 0.278 Chirality : 0.045 0.167 3633 Planarity : 0.004 0.045 4107 Dihedral : 4.588 33.560 3101 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.42 % Allowed : 12.16 % Favored : 85.42 % 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: 0.05 (0.15), residues: 2844 helix: 1.92 (0.20), residues: 664 sheet: -0.35 (0.19), residues: 607 loop : -0.61 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.003 0.001 HIS A1088 PHE 0.023 0.001 PHE B 168 TYR 0.021 0.001 TYR B1067 ARG 0.008 0.000 ARG C 237 *********************** 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 304 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 242 time to evaluate : 2.555 Fit side-chains REVERT: A 47 VAL cc_start: 0.5547 (t) cc_final: 0.5225 (p) REVERT: A 88 ASP cc_start: 0.6589 (OUTLIER) cc_final: 0.5980 (t0) REVERT: A 239 GLN cc_start: 0.5383 (tt0) cc_final: 0.5026 (tt0) REVERT: A 305 SER cc_start: 0.7282 (t) cc_final: 0.6843 (p) REVERT: A 314 GLN cc_start: 0.6501 (tt0) cc_final: 0.5877 (tp-100) REVERT: A 321 GLN cc_start: 0.6216 (mm-40) cc_final: 0.5911 (mp-120) REVERT: A 351 TYR cc_start: 0.4519 (p90) cc_final: 0.3891 (p90) REVERT: A 378 LYS cc_start: 0.4522 (pttm) cc_final: 0.4306 (pttm) REVERT: A 558 LYS cc_start: 0.7021 (tttt) cc_final: 0.6332 (mptp) REVERT: A 661 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6135 (mm-30) REVERT: A 674 TYR cc_start: 0.7555 (t80) cc_final: 0.7115 (t80) REVERT: A 702 GLU cc_start: 0.7283 (tt0) cc_final: 0.6786 (tp30) REVERT: A 779 GLN cc_start: 0.4867 (tp40) cc_final: 0.4445 (tp40) REVERT: A 814 LYS cc_start: 0.6291 (mttp) cc_final: 0.5772 (mtpt) REVERT: A 854 LYS cc_start: 0.2429 (mttp) cc_final: 0.2027 (ptpt) REVERT: A 912 THR cc_start: 0.7144 (OUTLIER) cc_final: 0.6902 (p) REVERT: A 1092 GLU cc_start: 0.5515 (mp0) cc_final: 0.5203 (mt-10) REVERT: A 1107 ARG cc_start: 0.6651 (mtm180) cc_final: 0.5698 (mtt180) REVERT: A 1128 VAL cc_start: 0.7544 (t) cc_final: 0.7143 (p) REVERT: B 52 GLN cc_start: 0.7192 (tt0) cc_final: 0.6619 (tp40) REVERT: B 271 GLN cc_start: 0.4335 (mt0) cc_final: 0.3858 (mp10) REVERT: B 314 GLN cc_start: 0.7327 (tt0) cc_final: 0.6586 (tp40) REVERT: B 319 ARG cc_start: 0.5887 (mtm180) cc_final: 0.5510 (ttm110) REVERT: B 324 GLU cc_start: 0.4177 (pt0) cc_final: 0.3618 (pm20) REVERT: B 534 VAL cc_start: 0.7549 (t) cc_final: 0.6990 (m) REVERT: B 568 ASP cc_start: 0.6215 (OUTLIER) cc_final: 0.5939 (m-30) REVERT: B 569 ILE cc_start: 0.6171 (mm) cc_final: 0.5879 (tt) REVERT: B 613 GLN cc_start: 0.6831 (mt0) cc_final: 0.6534 (mt0) REVERT: B 646 ARG cc_start: 0.6306 (ttm170) cc_final: 0.5284 (tpt170) REVERT: B 661 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6695 (mt-10) REVERT: B 697 MET cc_start: 0.7091 (ptp) cc_final: 0.6811 (ptp) REVERT: B 698 SER cc_start: 0.6806 (t) cc_final: 0.6296 (p) REVERT: B 702 GLU cc_start: 0.7039 (tt0) cc_final: 0.6563 (tp30) REVERT: B 735 SER cc_start: 0.6859 (t) cc_final: 0.6476 (t) REVERT: B 776 LYS cc_start: 0.4671 (tttt) cc_final: 0.3928 (tttm) REVERT: B 790 LYS cc_start: 0.6706 (pttt) cc_final: 0.6298 (ptmm) REVERT: B 814 LYS cc_start: 0.6611 (mttt) cc_final: 0.5491 (mmmt) REVERT: B 912 THR cc_start: 0.6789 (OUTLIER) cc_final: 0.6443 (p) REVERT: B 988 GLU cc_start: 0.4929 (tp30) cc_final: 0.4409 (mp0) REVERT: B 1010 GLN cc_start: 0.4781 (mm-40) cc_final: 0.3763 (pt0) REVERT: B 1045 LYS cc_start: 0.6781 (ttpp) cc_final: 0.5899 (mptp) REVERT: B 1074 ASN cc_start: 0.5867 (m-40) cc_final: 0.5523 (m-40) REVERT: C 281 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6513 (pm20) REVERT: C 305 SER cc_start: 0.6930 (t) cc_final: 0.6461 (p) REVERT: C 317 ASN cc_start: 0.7372 (t0) cc_final: 0.7082 (t0) REVERT: C 359 SER cc_start: 0.6817 (p) cc_final: 0.6432 (m) REVERT: C 378 LYS cc_start: 0.6209 (OUTLIER) cc_final: 0.5749 (mtmt) REVERT: C 383 CYS cc_start: 0.4641 (t) cc_final: 0.4121 (t) REVERT: C 396 TYR cc_start: 0.4689 (m-80) cc_final: 0.4178 (m-80) REVERT: C 424 LYS cc_start: 0.4140 (tptp) cc_final: 0.3721 (tptp) REVERT: C 516 GLU cc_start: 0.5630 (tp30) cc_final: 0.5419 (tp30) REVERT: C 528 LYS cc_start: 0.5796 (tttt) cc_final: 0.5140 (tppt) REVERT: C 564 GLN cc_start: 0.5842 (tp40) cc_final: 0.5484 (mp-120) REVERT: C 569 ILE cc_start: 0.6548 (mm) cc_final: 0.6110 (tp) REVERT: C 675 GLN cc_start: 0.5395 (mt0) cc_final: 0.4840 (mt0) REVERT: C 702 GLU cc_start: 0.7656 (tt0) cc_final: 0.7128 (tp30) REVERT: C 704 SER cc_start: 0.7470 (p) cc_final: 0.7150 (t) REVERT: C 776 LYS cc_start: 0.5331 (tttt) cc_final: 0.5062 (ttmp) REVERT: C 790 LYS cc_start: 0.6416 (pttt) cc_final: 0.5571 (mttp) REVERT: C 814 LYS cc_start: 0.5917 (mttt) cc_final: 0.5176 (mtpt) REVERT: C 912 THR cc_start: 0.6843 (OUTLIER) cc_final: 0.6501 (p) REVERT: C 950 ASP cc_start: 0.5820 (m-30) cc_final: 0.5558 (m-30) REVERT: C 990 GLU cc_start: 0.3757 (mt-10) cc_final: 0.3303 (mp0) REVERT: C 995 ARG cc_start: 0.3955 (mtt180) cc_final: 0.3734 (mtp180) REVERT: C 1010 GLN cc_start: 0.5154 (mm-40) cc_final: 0.4241 (pt0) outliers start: 62 outliers final: 37 residues processed: 283 average time/residue: 0.9624 time to fit residues: 327.3558 Evaluate side-chains 279 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 2.317 ------------------------------------------------------------------------------- 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 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 649 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR 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 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 568 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain C residue 281 GLU 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 727 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 985 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 191 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 220 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A1119 ASN B 394 ASN B1119 ASN C 196 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4558 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 23325 Z= 0.361 Angle : 0.592 9.669 31740 Z= 0.310 Chirality : 0.047 0.163 3633 Planarity : 0.004 0.048 4107 Dihedral : 4.896 42.319 3101 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.65 % Allowed : 12.48 % Favored : 84.87 % 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: -0.23 (0.15), residues: 2844 helix: 1.55 (0.20), residues: 672 sheet: -0.50 (0.19), residues: 637 loop : -0.74 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 436 HIS 0.006 0.001 HIS C1048 PHE 0.017 0.002 PHE C 238 TYR 0.025 0.002 TYR B 170 ARG 0.007 0.000 ARG C 237 *********************** 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 302 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 234 time to evaluate : 2.606 Fit side-chains REVERT: A 47 VAL cc_start: 0.5503 (t) cc_final: 0.5157 (p) REVERT: A 88 ASP cc_start: 0.6590 (OUTLIER) cc_final: 0.5987 (t0) REVERT: A 239 GLN cc_start: 0.5316 (tt0) cc_final: 0.4967 (tt0) REVERT: A 305 SER cc_start: 0.7223 (t) cc_final: 0.6762 (p) REVERT: A 314 GLN cc_start: 0.6275 (tt0) cc_final: 0.5726 (tp-100) REVERT: A 321 GLN cc_start: 0.6185 (mm-40) cc_final: 0.5892 (mp-120) REVERT: A 351 TYR cc_start: 0.4514 (p90) cc_final: 0.3870 (p90) REVERT: A 378 LYS cc_start: 0.4546 (pttm) cc_final: 0.4322 (pttm) REVERT: A 558 LYS cc_start: 0.7050 (tttt) cc_final: 0.6401 (mptp) REVERT: A 603 ASN cc_start: 0.6769 (t0) cc_final: 0.6365 (m110) REVERT: A 654 GLU cc_start: 0.5434 (tt0) cc_final: 0.4987 (tm-30) REVERT: A 661 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6175 (mm-30) REVERT: A 702 GLU cc_start: 0.7320 (tt0) cc_final: 0.6823 (tp30) REVERT: A 740 MET cc_start: 0.5506 (OUTLIER) cc_final: 0.5245 (ttp) REVERT: A 779 GLN cc_start: 0.4892 (tp40) cc_final: 0.4521 (tp40) REVERT: A 814 LYS cc_start: 0.6321 (mttp) cc_final: 0.5846 (mtpt) REVERT: A 854 LYS cc_start: 0.2441 (mttp) cc_final: 0.2019 (ptpt) REVERT: A 912 THR cc_start: 0.7030 (OUTLIER) cc_final: 0.6803 (p) REVERT: A 1092 GLU cc_start: 0.5844 (mp0) cc_final: 0.5486 (mt-10) REVERT: A 1107 ARG cc_start: 0.6686 (mtm180) cc_final: 0.5741 (mpt-90) REVERT: A 1128 VAL cc_start: 0.7506 (t) cc_final: 0.7075 (p) REVERT: B 52 GLN cc_start: 0.7190 (tt0) cc_final: 0.6622 (tp40) REVERT: B 271 GLN cc_start: 0.4164 (mt0) cc_final: 0.3678 (mp10) REVERT: B 314 GLN cc_start: 0.7352 (tt0) cc_final: 0.6605 (tp40) REVERT: B 319 ARG cc_start: 0.5988 (mtm180) cc_final: 0.5633 (ttm110) REVERT: B 324 GLU cc_start: 0.4183 (pt0) cc_final: 0.3625 (pm20) REVERT: B 534 VAL cc_start: 0.7655 (t) cc_final: 0.7087 (m) REVERT: B 564 GLN cc_start: 0.4438 (OUTLIER) cc_final: 0.3795 (mm-40) REVERT: B 569 ILE cc_start: 0.6087 (mm) cc_final: 0.5624 (tt) REVERT: B 574 ASP cc_start: 0.4819 (t0) cc_final: 0.4536 (t0) REVERT: B 613 GLN cc_start: 0.6601 (mt0) cc_final: 0.6291 (mt0) REVERT: B 646 ARG cc_start: 0.6426 (ttm170) cc_final: 0.5338 (tpt170) REVERT: B 661 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6689 (mt-10) REVERT: B 697 MET cc_start: 0.7116 (ptp) cc_final: 0.6899 (ptp) REVERT: B 698 SER cc_start: 0.6791 (t) cc_final: 0.6297 (p) REVERT: B 702 GLU cc_start: 0.7105 (tt0) cc_final: 0.6605 (tp30) REVERT: B 735 SER cc_start: 0.6834 (t) cc_final: 0.6462 (t) REVERT: B 790 LYS cc_start: 0.6736 (pttt) cc_final: 0.6294 (ptmm) REVERT: B 814 LYS cc_start: 0.6583 (mttt) cc_final: 0.5633 (mmmt) REVERT: B 912 THR cc_start: 0.6816 (OUTLIER) cc_final: 0.6460 (p) REVERT: B 988 GLU cc_start: 0.4846 (tp30) cc_final: 0.4391 (mp0) REVERT: B 1010 GLN cc_start: 0.4841 (mm-40) cc_final: 0.3854 (pt0) REVERT: B 1045 LYS cc_start: 0.6721 (ttpp) cc_final: 0.5906 (mptp) REVERT: C 281 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6556 (pm20) REVERT: C 305 SER cc_start: 0.6859 (t) cc_final: 0.6316 (p) REVERT: C 378 LYS cc_start: 0.6133 (OUTLIER) cc_final: 0.5729 (mtmt) REVERT: C 382 VAL cc_start: 0.5319 (t) cc_final: 0.5100 (p) REVERT: C 383 CYS cc_start: 0.4789 (t) cc_final: 0.4366 (t) REVERT: C 396 TYR cc_start: 0.4756 (m-80) cc_final: 0.4212 (m-80) REVERT: C 424 LYS cc_start: 0.4254 (tptp) cc_final: 0.3868 (tptp) REVERT: C 528 LYS cc_start: 0.5680 (tttt) cc_final: 0.5073 (tppt) REVERT: C 569 ILE cc_start: 0.6589 (mm) cc_final: 0.6098 (tp) REVERT: C 675 GLN cc_start: 0.5422 (mt0) cc_final: 0.4882 (mt0) REVERT: C 702 GLU cc_start: 0.7682 (tt0) cc_final: 0.6880 (tp30) REVERT: C 776 LYS cc_start: 0.5354 (tttt) cc_final: 0.5097 (ttmp) REVERT: C 790 LYS cc_start: 0.6538 (pttt) cc_final: 0.5701 (mttp) REVERT: C 814 LYS cc_start: 0.6035 (mttt) cc_final: 0.5334 (mtpt) REVERT: C 912 THR cc_start: 0.6709 (OUTLIER) cc_final: 0.6348 (p) REVERT: C 950 ASP cc_start: 0.5709 (m-30) cc_final: 0.5493 (m-30) REVERT: C 990 GLU cc_start: 0.3850 (mt-10) cc_final: 0.3335 (mp0) REVERT: C 1010 GLN cc_start: 0.5152 (mm-40) cc_final: 0.4228 (pt0) REVERT: C 1106 GLN cc_start: 0.6416 (OUTLIER) cc_final: 0.6144 (pt0) outliers start: 68 outliers final: 42 residues processed: 282 average time/residue: 0.9237 time to fit residues: 314.7757 Evaluate side-chains 279 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 228 time to evaluate : 2.643 ------------------------------------------------------------------------------- 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 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 649 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR 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 1105 THR 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 287 ASP 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 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 336 CYS 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 727 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 985 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1133 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 255 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 chunk 261 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 236 optimal weight: 0.7980 chunk 247 optimal weight: 5.9990 chunk 260 optimal weight: 0.0770 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A1119 ASN B 957 GLN C 196 ASN C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4536 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 23325 Z= 0.197 Angle : 0.515 7.432 31740 Z= 0.272 Chirality : 0.045 0.165 3633 Planarity : 0.004 0.047 4107 Dihedral : 4.576 37.906 3101 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.99 % Allowed : 13.29 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 2844 helix: 1.92 (0.20), residues: 667 sheet: -0.38 (0.20), residues: 603 loop : -0.64 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.002 0.001 HIS A1088 PHE 0.017 0.001 PHE C 65 TYR 0.020 0.001 TYR B1067 ARG 0.007 0.000 ARG C 237 *********************** 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 291 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 240 time to evaluate : 2.619 Fit side-chains REVERT: A 47 VAL cc_start: 0.5543 (t) cc_final: 0.5205 (p) REVERT: A 88 ASP cc_start: 0.6595 (OUTLIER) cc_final: 0.6024 (t0) REVERT: A 239 GLN cc_start: 0.5349 (tt0) cc_final: 0.4994 (tt0) REVERT: A 305 SER cc_start: 0.7288 (t) cc_final: 0.6873 (p) REVERT: A 314 GLN cc_start: 0.6550 (tt0) cc_final: 0.5941 (tp-100) REVERT: A 351 TYR cc_start: 0.4507 (p90) cc_final: 0.3863 (p90) REVERT: A 378 LYS cc_start: 0.4570 (pttm) cc_final: 0.4343 (pttm) REVERT: A 558 LYS cc_start: 0.7055 (tttt) cc_final: 0.6364 (mptp) REVERT: A 654 GLU cc_start: 0.5390 (tt0) cc_final: 0.4964 (tm-30) REVERT: A 661 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6120 (mm-30) REVERT: A 674 TYR cc_start: 0.7558 (t80) cc_final: 0.7027 (t80) REVERT: A 702 GLU cc_start: 0.7436 (tt0) cc_final: 0.6898 (tp30) REVERT: A 779 GLN cc_start: 0.4854 (tp40) cc_final: 0.4448 (tp40) REVERT: A 814 LYS cc_start: 0.6422 (mttp) cc_final: 0.5898 (mtpt) REVERT: A 854 LYS cc_start: 0.2429 (mttp) cc_final: 0.1930 (ptpt) REVERT: A 1092 GLU cc_start: 0.5764 (mp0) cc_final: 0.5357 (mt-10) REVERT: A 1107 ARG cc_start: 0.6537 (mtm180) cc_final: 0.5623 (mtt180) REVERT: A 1128 VAL cc_start: 0.7506 (t) cc_final: 0.7070 (p) REVERT: B 52 GLN cc_start: 0.7170 (tt0) cc_final: 0.6610 (tp40) REVERT: B 271 GLN cc_start: 0.4309 (mt0) cc_final: 0.3833 (mp10) REVERT: B 314 GLN cc_start: 0.7327 (tt0) cc_final: 0.6594 (tp40) REVERT: B 319 ARG cc_start: 0.5954 (mtm180) cc_final: 0.5580 (ttm110) REVERT: B 324 GLU cc_start: 0.4216 (pt0) cc_final: 0.3648 (pm20) REVERT: B 534 VAL cc_start: 0.7678 (t) cc_final: 0.7169 (m) REVERT: B 613 GLN cc_start: 0.6675 (mt0) cc_final: 0.6382 (mt0) REVERT: B 646 ARG cc_start: 0.6353 (ttm170) cc_final: 0.5294 (tpt170) REVERT: B 661 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6680 (mt-10) REVERT: B 698 SER cc_start: 0.6797 (t) cc_final: 0.6302 (p) REVERT: B 702 GLU cc_start: 0.7031 (tt0) cc_final: 0.6585 (tp30) REVERT: B 735 SER cc_start: 0.7006 (t) cc_final: 0.6188 (p) REVERT: B 790 LYS cc_start: 0.6743 (pttt) cc_final: 0.6390 (ptmm) REVERT: B 814 LYS cc_start: 0.6635 (mttt) cc_final: 0.5658 (mmmt) REVERT: B 912 THR cc_start: 0.6789 (OUTLIER) cc_final: 0.6431 (p) REVERT: B 988 GLU cc_start: 0.4914 (tp30) cc_final: 0.4413 (mp0) REVERT: B 1010 GLN cc_start: 0.4855 (mm-40) cc_final: 0.3839 (pt0) REVERT: B 1045 LYS cc_start: 0.6825 (ttpp) cc_final: 0.5965 (mptp) REVERT: B 1074 ASN cc_start: 0.5982 (m-40) cc_final: 0.5656 (m-40) REVERT: B 1119 ASN cc_start: 0.5724 (m110) cc_final: 0.5354 (m110) REVERT: C 305 SER cc_start: 0.6963 (t) cc_final: 0.6470 (p) REVERT: C 359 SER cc_start: 0.6699 (p) cc_final: 0.6247 (m) REVERT: C 378 LYS cc_start: 0.6202 (OUTLIER) cc_final: 0.5778 (mtmt) REVERT: C 382 VAL cc_start: 0.5113 (t) cc_final: 0.4901 (p) REVERT: C 383 CYS cc_start: 0.4800 (t) cc_final: 0.4343 (t) REVERT: C 396 TYR cc_start: 0.4751 (m-80) cc_final: 0.4252 (m-80) REVERT: C 424 LYS cc_start: 0.4084 (tptp) cc_final: 0.3784 (tptp) REVERT: C 516 GLU cc_start: 0.5207 (tp30) cc_final: 0.4946 (tp30) REVERT: C 528 LYS cc_start: 0.5684 (tttt) cc_final: 0.5067 (tppt) REVERT: C 564 GLN cc_start: 0.5872 (tp40) cc_final: 0.5516 (mp-120) REVERT: C 569 ILE cc_start: 0.6604 (mm) cc_final: 0.6139 (tp) REVERT: C 675 GLN cc_start: 0.5424 (mt0) cc_final: 0.4856 (mt0) REVERT: C 702 GLU cc_start: 0.7690 (tt0) cc_final: 0.6946 (tp30) REVERT: C 776 LYS cc_start: 0.5359 (tttt) cc_final: 0.5089 (ttmp) REVERT: C 790 LYS cc_start: 0.6544 (pttt) cc_final: 0.5721 (mttp) REVERT: C 814 LYS cc_start: 0.5939 (mttt) cc_final: 0.5179 (mtpt) REVERT: C 912 THR cc_start: 0.6855 (OUTLIER) cc_final: 0.6515 (p) REVERT: C 950 ASP cc_start: 0.5828 (m-30) cc_final: 0.5564 (m-30) REVERT: C 990 GLU cc_start: 0.3794 (mt-10) cc_final: 0.3330 (mp0) REVERT: C 1010 GLN cc_start: 0.5127 (mm-40) cc_final: 0.4116 (pt0) outliers start: 51 outliers final: 38 residues processed: 278 average time/residue: 0.9018 time to fit residues: 305.0963 Evaluate side-chains 272 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 230 time to evaluate : 2.439 ------------------------------------------------------------------------------- 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 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 861 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1004 LEU 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 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 336 CYS 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 859 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 985 CYS 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 171 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 192 optimal weight: 0.9980 chunk 289 optimal weight: 0.7980 chunk 266 optimal weight: 1.9990 chunk 230 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 178 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN C 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4542 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 23325 Z= 0.227 Angle : 0.525 7.526 31740 Z= 0.277 Chirality : 0.045 0.163 3633 Planarity : 0.004 0.047 4107 Dihedral : 4.555 37.547 3101 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.87 % Allowed : 13.49 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 2844 helix: 1.91 (0.20), residues: 667 sheet: -0.36 (0.20), residues: 603 loop : -0.63 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.003 0.001 HIS A1088 PHE 0.016 0.001 PHE C 65 TYR 0.020 0.001 TYR B1067 ARG 0.006 0.000 ARG C 237 ********************** 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 281 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 233 time to evaluate : 2.618 Fit side-chains REVERT: A 47 VAL cc_start: 0.5448 (t) cc_final: 0.5104 (p) REVERT: A 88 ASP cc_start: 0.6595 (OUTLIER) cc_final: 0.6032 (t0) REVERT: A 239 GLN cc_start: 0.5351 (tt0) cc_final: 0.4999 (tt0) REVERT: A 305 SER cc_start: 0.7205 (t) cc_final: 0.6812 (p) REVERT: A 314 GLN cc_start: 0.6497 (tt0) cc_final: 0.5901 (tp-100) REVERT: A 351 TYR cc_start: 0.4501 (p90) cc_final: 0.3857 (p90) REVERT: A 378 LYS cc_start: 0.4575 (pttm) cc_final: 0.4348 (pttm) REVERT: A 558 LYS cc_start: 0.6957 (tttt) cc_final: 0.6364 (mptp) REVERT: A 654 GLU cc_start: 0.5399 (tt0) cc_final: 0.4961 (tm-30) REVERT: A 661 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6166 (mm-30) REVERT: A 674 TYR cc_start: 0.7564 (t80) cc_final: 0.7032 (t80) REVERT: A 702 GLU cc_start: 0.7423 (tt0) cc_final: 0.6895 (tp30) REVERT: A 779 GLN cc_start: 0.4864 (tp40) cc_final: 0.4447 (tp40) REVERT: A 814 LYS cc_start: 0.6514 (mttp) cc_final: 0.5921 (mtpt) REVERT: A 854 LYS cc_start: 0.2407 (mttp) cc_final: 0.1904 (ptpt) REVERT: A 1092 GLU cc_start: 0.5788 (mp0) cc_final: 0.5374 (mt-10) REVERT: A 1107 ARG cc_start: 0.6598 (mtm180) cc_final: 0.5623 (mtt180) REVERT: A 1128 VAL cc_start: 0.7506 (t) cc_final: 0.7076 (p) REVERT: B 52 GLN cc_start: 0.7166 (tt0) cc_final: 0.6605 (tp40) REVERT: B 271 GLN cc_start: 0.4312 (mt0) cc_final: 0.3837 (mp10) REVERT: B 314 GLN cc_start: 0.7390 (tt0) cc_final: 0.6657 (tp40) REVERT: B 319 ARG cc_start: 0.5940 (mtm180) cc_final: 0.5582 (ttm110) REVERT: B 324 GLU cc_start: 0.4209 (pt0) cc_final: 0.3648 (pm20) REVERT: B 534 VAL cc_start: 0.7695 (t) cc_final: 0.7165 (m) REVERT: B 613 GLN cc_start: 0.6631 (mt0) cc_final: 0.6334 (mt0) REVERT: B 646 ARG cc_start: 0.6367 (ttm170) cc_final: 0.5301 (tpt170) REVERT: B 661 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6669 (mt-10) REVERT: B 698 SER cc_start: 0.6810 (t) cc_final: 0.6331 (p) REVERT: B 735 SER cc_start: 0.6956 (t) cc_final: 0.6560 (t) REVERT: B 776 LYS cc_start: 0.4682 (tttt) cc_final: 0.3950 (tttm) REVERT: B 790 LYS cc_start: 0.6618 (pttt) cc_final: 0.6244 (ptmm) REVERT: B 814 LYS cc_start: 0.6645 (mttt) cc_final: 0.5666 (mmmt) REVERT: B 912 THR cc_start: 0.6825 (OUTLIER) cc_final: 0.6463 (p) REVERT: B 988 GLU cc_start: 0.4906 (tp30) cc_final: 0.4411 (mp0) REVERT: B 1010 GLN cc_start: 0.4849 (mm-40) cc_final: 0.3836 (pt0) REVERT: B 1045 LYS cc_start: 0.6797 (ttpp) cc_final: 0.5932 (mptp) REVERT: B 1074 ASN cc_start: 0.5961 (m-40) cc_final: 0.5625 (m-40) REVERT: B 1119 ASN cc_start: 0.5791 (m110) cc_final: 0.5415 (m110) REVERT: C 305 SER cc_start: 0.6954 (t) cc_final: 0.6463 (p) REVERT: C 359 SER cc_start: 0.6706 (p) cc_final: 0.6254 (m) REVERT: C 378 LYS cc_start: 0.6198 (OUTLIER) cc_final: 0.5774 (mtmt) REVERT: C 382 VAL cc_start: 0.5250 (t) cc_final: 0.5041 (p) REVERT: C 383 CYS cc_start: 0.4888 (t) cc_final: 0.4436 (t) REVERT: C 396 TYR cc_start: 0.4579 (m-80) cc_final: 0.4083 (m-80) REVERT: C 424 LYS cc_start: 0.4084 (tptp) cc_final: 0.3780 (tptp) REVERT: C 516 GLU cc_start: 0.5186 (tp30) cc_final: 0.4927 (tp30) REVERT: C 528 LYS cc_start: 0.5716 (tttt) cc_final: 0.5087 (tppt) REVERT: C 564 GLN cc_start: 0.5881 (tp40) cc_final: 0.5532 (mp-120) REVERT: C 569 ILE cc_start: 0.6607 (mm) cc_final: 0.6143 (tp) REVERT: C 582 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6954 (mm) REVERT: C 675 GLN cc_start: 0.5431 (mt0) cc_final: 0.4874 (mt0) REVERT: C 702 GLU cc_start: 0.7690 (tt0) cc_final: 0.7092 (tp30) REVERT: C 704 SER cc_start: 0.7465 (p) cc_final: 0.7140 (t) REVERT: C 776 LYS cc_start: 0.5332 (tttt) cc_final: 0.5067 (ttmp) REVERT: C 790 LYS cc_start: 0.6547 (pttt) cc_final: 0.5703 (mttt) REVERT: C 814 LYS cc_start: 0.5926 (mttt) cc_final: 0.5179 (mtpt) REVERT: C 912 THR cc_start: 0.6862 (OUTLIER) cc_final: 0.6481 (p) REVERT: C 950 ASP cc_start: 0.5838 (m-30) cc_final: 0.5574 (m-30) REVERT: C 990 GLU cc_start: 0.3810 (mt-10) cc_final: 0.3300 (mp0) REVERT: C 1010 GLN cc_start: 0.5130 (mm-40) cc_final: 0.4220 (pt0) REVERT: C 1106 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5936 (pt0) outliers start: 48 outliers final: 37 residues processed: 266 average time/residue: 0.9652 time to fit residues: 308.3366 Evaluate side-chains 269 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 226 time to evaluate : 2.302 ------------------------------------------------------------------------------- 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 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 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 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 985 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 336 CYS 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 582 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 985 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1106 GLN 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 183 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 212 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 231 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 237 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.213822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151330 restraints weight = 22244.925| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.86 r_work: 0.3698 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 23325 Z= 0.241 Angle : 0.528 7.501 31740 Z= 0.277 Chirality : 0.045 0.163 3633 Planarity : 0.004 0.047 4107 Dihedral : 4.552 37.923 3101 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.95 % Allowed : 13.37 % Favored : 84.68 % 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: 1.89 (0.20), residues: 667 sheet: -0.39 (0.20), residues: 605 loop : -0.63 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS B1048 PHE 0.016 0.001 PHE C 65 TYR 0.026 0.001 TYR B 170 ARG 0.006 0.000 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7065.34 seconds wall clock time: 125 minutes 1.31 seconds (7501.31 seconds total)