Starting phenix.real_space_refine on Thu Mar 5 13:59:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x2c_22001/03_2026/6x2c_22001_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x2c_22001/03_2026/6x2c_22001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x2c_22001/03_2026/6x2c_22001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x2c_22001/03_2026/6x2c_22001.map" model { file = "/net/cci-nas-00/data/ceres_data/6x2c_22001/03_2026/6x2c_22001_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x2c_22001/03_2026/6x2c_22001_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.063 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 99 5.16 5 C 14586 2.51 5 N 3777 2.21 5 O 4338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22800 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7600 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 11 Chain: "B" Number of atoms: 7600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7600 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 11 Chain: "C" Number of atoms: 7600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7600 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 11 Time building chain proxies: 4.43, per 1000 atoms: 0.19 Number of scatterers: 22800 At special positions: 0 Unit cell: (132.25, 138.598, 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 99 16.00 O 4338 8.00 N 3777 7.00 C 14586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.01 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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: 1.65 Conformation dependent library (CDL) restraints added in 959.2 milliseconds 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5478 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 51 sheets defined 27.7% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.945A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.854A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.326A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.693A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.711A 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: 3.898A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.391A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.600A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.502A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.556A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.683A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (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: 4.064A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.394A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 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: 3.947A 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: 4.816A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.314A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.711A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.781A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) 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: 3.911A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.403A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.612A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (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 918 removed outlier: 3.540A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.665A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.064A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.434A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.964A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.901A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.310A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.694A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.627A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) 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: 3.911A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.409A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.594A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.530A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.677A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.064A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.449A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.799A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 5.675A 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: 5.594A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.594A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.764A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.465A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.511A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.292A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.571A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.604A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 356 Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.685A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.010A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.803A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 722 removed outlier: 5.778A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.301A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.090A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.774A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.472A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.593A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.593A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.759A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.466A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.519A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.286A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 356 Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.689A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.021A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.813A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 5.790A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 788 through 790 removed outlier: 6.299A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.092A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.776A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.770A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.455A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.516A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.294A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.689A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.014A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.811A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 722 removed outlier: 5.792A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.107A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1053 hydrogen bonds defined for protein. 2829 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: 5.62 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6228 1.34 - 1.46: 4199 1.46 - 1.58: 12754 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 23304 Sorted by residual: bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.541 -0.024 6.70e-03 2.23e+04 1.26e+01 bond pdb=" CA ASN B 422 " pdb=" C ASN B 422 " ideal model delta sigma weight residual 1.517 1.539 -0.022 6.30e-03 2.52e+04 1.23e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.539 -0.022 6.70e-03 2.23e+04 1.12e+01 bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.539 -0.022 6.70e-03 2.23e+04 1.08e+01 bond pdb=" CA ALA A 411 " pdb=" C ALA A 411 " ideal model delta sigma weight residual 1.519 1.549 -0.030 9.50e-03 1.11e+04 9.76e+00 ... (remaining 23299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 18943 1.46 - 2.92: 9263 2.92 - 4.38: 2932 4.38 - 5.85: 510 5.85 - 7.31: 56 Bond angle restraints: 31704 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 117.92 -7.22 1.22e+00 6.72e-01 3.50e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.89 -7.19 1.22e+00 6.72e-01 3.48e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 117.80 -7.10 1.22e+00 6.72e-01 3.38e+01 angle pdb=" CA ASP B 568 " pdb=" CB ASP B 568 " pdb=" CG ASP B 568 " ideal model delta sigma weight residual 112.60 118.29 -5.69 1.00e+00 1.00e+00 3.24e+01 angle pdb=" CA ASP A 228 " pdb=" CB ASP A 228 " pdb=" CG ASP A 228 " ideal model delta sigma weight residual 112.60 118.27 -5.67 1.00e+00 1.00e+00 3.21e+01 ... (remaining 31699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 12811 17.35 - 34.70: 852 34.70 - 52.04: 138 52.04 - 69.39: 78 69.39 - 86.74: 17 Dihedral angle restraints: 13896 sinusoidal: 5412 harmonic: 8484 Sorted by residual: dihedral pdb=" CA TYR A 451 " pdb=" C TYR A 451 " pdb=" N LEU A 452 " pdb=" CA LEU A 452 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA TYR C 451 " pdb=" C TYR C 451 " pdb=" N LEU C 452 " pdb=" CA LEU C 452 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA TYR B 451 " pdb=" C TYR B 451 " pdb=" N LEU B 452 " pdb=" CA LEU B 452 " ideal model delta harmonic sigma weight residual 180.00 -151.27 -28.73 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 13893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2031 0.073 - 0.146: 1256 0.146 - 0.219: 280 0.219 - 0.292: 54 0.292 - 0.365: 15 Chirality restraints: 3636 Sorted by residual: chirality pdb=" CA GLU C 773 " pdb=" N GLU C 773 " pdb=" C GLU C 773 " pdb=" CB GLU C 773 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA ASP B 568 " pdb=" N ASP B 568 " pdb=" C ASP B 568 " pdb=" CB ASP B 568 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA ASP A 568 " pdb=" N ASP A 568 " pdb=" C ASP A 568 " pdb=" CB ASP A 568 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 3633 not shown) Planarity restraints: 4095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 423 " -0.135 2.00e-02 2.50e+03 7.25e-02 1.05e+02 pdb=" CG TYR B 423 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 423 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR B 423 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR B 423 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR B 423 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR B 423 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 423 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 423 " -0.132 2.00e-02 2.50e+03 7.09e-02 1.01e+02 pdb=" CG TYR A 423 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 423 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR A 423 " 0.057 2.00e-02 2.50e+03 pdb=" CE1 TYR A 423 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR A 423 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR A 423 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 423 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 423 " -0.127 2.00e-02 2.50e+03 6.83e-02 9.32e+01 pdb=" CG TYR C 423 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR C 423 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 TYR C 423 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR C 423 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR C 423 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR C 423 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 423 " -0.101 2.00e-02 2.50e+03 ... (remaining 4092 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 11573 3.02 - 3.49: 21525 3.49 - 3.96: 37236 3.96 - 4.43: 41793 4.43 - 4.90: 71634 Nonbonded interactions: 183761 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU C 918 " model vdw 2.550 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER B1123 " model vdw 2.557 3.040 nonbonded pdb=" OE2 GLU B 918 " pdb=" OG SER C1123 " model vdw 2.561 3.040 nonbonded pdb=" OD1 ASP C 294 " pdb=" OG SER C 297 " model vdw 2.568 3.040 nonbonded pdb=" OD1 ASP B 294 " pdb=" OG SER B 297 " model vdw 2.571 3.040 ... (remaining 183756 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: 0.05 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: 1.750 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.770 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 0.043 23340 Z= 0.743 Angle : 1.808 7.308 31776 Z= 1.225 Chirality : 0.093 0.365 3636 Planarity : 0.016 0.220 4095 Dihedral : 13.390 86.741 8310 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 0.20 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.32 % Favored : 94.37 % Rotamer: Outliers : 3.17 % Allowed : 4.77 % Favored : 92.06 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.14), residues: 2841 helix: -1.64 (0.17), residues: 630 sheet: -0.66 (0.19), residues: 603 loop : -1.09 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG C1107 TYR 0.135 0.022 TYR B 423 PHE 0.070 0.011 PHE C 718 TRP 0.069 0.018 TRP C1102 HIS 0.011 0.003 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.01264 (23304) covalent geometry : angle 1.80790 (31704) SS BOND : bond 0.01090 ( 36) SS BOND : angle 1.94139 ( 72) hydrogen bonds : bond 0.16442 ( 1006) hydrogen bonds : angle 8.83494 ( 2829) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 252 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7785 (t60) cc_final: 0.7571 (t60) REVERT: A 133 PHE cc_start: 0.7918 (m-80) cc_final: 0.7605 (m-80) REVERT: A 392 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: A 574 ASP cc_start: 0.7396 (t0) cc_final: 0.7159 (t0) REVERT: B 64 TRP cc_start: 0.7874 (t60) cc_final: 0.7571 (t60) REVERT: B 353 TRP cc_start: 0.7867 (p-90) cc_final: 0.7250 (p-90) REVERT: B 399 SER cc_start: 0.8314 (OUTLIER) cc_final: 0.7882 (t) REVERT: B 434 ILE cc_start: 0.8951 (mt) cc_final: 0.8628 (tp) REVERT: B 453 TYR cc_start: 0.7564 (p90) cc_final: 0.7229 (p90) REVERT: B 574 ASP cc_start: 0.7437 (t0) cc_final: 0.7179 (t0) REVERT: B 1004 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8838 (tt) REVERT: C 64 TRP cc_start: 0.7752 (t60) cc_final: 0.7470 (t60) REVERT: C 434 ILE cc_start: 0.8969 (mt) cc_final: 0.8650 (tp) REVERT: C 574 ASP cc_start: 0.7353 (t0) cc_final: 0.7113 (t0) outliers start: 81 outliers final: 38 residues processed: 317 average time/residue: 0.1553 time to fit residues: 76.8113 Evaluate side-chains 177 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 894 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.0570 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 955 ASN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.138782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.101980 restraints weight = 41488.409| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.68 r_work: 0.3364 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23340 Z= 0.137 Angle : 0.596 7.438 31776 Z= 0.321 Chirality : 0.046 0.174 3636 Planarity : 0.004 0.038 4095 Dihedral : 7.389 59.334 3166 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.70 % Allowed : 6.89 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 2841 helix: 0.66 (0.20), residues: 639 sheet: -0.12 (0.19), residues: 642 loop : -0.68 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.017 0.001 TYR A1067 PHE 0.022 0.002 PHE C 140 TRP 0.016 0.002 TRP C 64 HIS 0.002 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00295 (23304) covalent geometry : angle 0.59545 (31704) SS BOND : bond 0.00243 ( 36) SS BOND : angle 0.76990 ( 72) hydrogen bonds : bond 0.04197 ( 1006) hydrogen bonds : angle 5.99491 ( 2829) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 162 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7762 (m-90) cc_final: 0.7430 (m-90) REVERT: A 133 PHE cc_start: 0.7888 (m-80) cc_final: 0.7425 (m-80) REVERT: A 378 LYS cc_start: 0.8332 (ttmm) cc_final: 0.8130 (ttmm) REVERT: A 392 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7097 (m-80) REVERT: A 574 ASP cc_start: 0.8063 (t0) cc_final: 0.7626 (t0) REVERT: A 985 ASP cc_start: 0.7911 (p0) cc_final: 0.6817 (p0) REVERT: B 133 PHE cc_start: 0.7790 (m-80) cc_final: 0.6349 (t80) REVERT: B 226 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8371 (tp) REVERT: B 353 TRP cc_start: 0.7820 (p-90) cc_final: 0.7359 (p-90) REVERT: B 434 ILE cc_start: 0.8769 (mt) cc_final: 0.8120 (tp) REVERT: B 574 ASP cc_start: 0.8096 (t0) cc_final: 0.7577 (t0) REVERT: B 869 MET cc_start: 0.9165 (mtt) cc_final: 0.8898 (mtp) REVERT: B 985 ASP cc_start: 0.8042 (p0) cc_final: 0.7045 (p0) REVERT: B 1004 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8996 (tt) REVERT: C 104 TRP cc_start: 0.7853 (m-90) cc_final: 0.7413 (m-90) REVERT: C 133 PHE cc_start: 0.7585 (m-80) cc_final: 0.7159 (m-80) REVERT: C 389 ASP cc_start: 0.7551 (t0) cc_final: 0.7314 (t0) REVERT: C 574 ASP cc_start: 0.7962 (t70) cc_final: 0.7467 (t0) outliers start: 69 outliers final: 44 residues processed: 214 average time/residue: 0.1575 time to fit residues: 53.3778 Evaluate side-chains 174 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 282 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 220 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.125750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.094289 restraints weight = 39430.742| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.68 r_work: 0.3163 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23340 Z= 0.198 Angle : 0.567 7.275 31776 Z= 0.301 Chirality : 0.046 0.163 3636 Planarity : 0.004 0.041 4095 Dihedral : 6.651 57.025 3159 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.78 % Allowed : 8.18 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.16), residues: 2841 helix: 1.38 (0.21), residues: 639 sheet: -0.13 (0.19), residues: 654 loop : -0.61 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 567 TYR 0.019 0.001 TYR C1067 PHE 0.018 0.002 PHE C1089 TRP 0.012 0.001 TRP B 104 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00472 (23304) covalent geometry : angle 0.56629 (31704) SS BOND : bond 0.00300 ( 36) SS BOND : angle 0.88750 ( 72) hydrogen bonds : bond 0.03911 ( 1006) hydrogen bonds : angle 5.58467 ( 2829) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 143 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7903 (m-90) cc_final: 0.7457 (m-90) REVERT: A 133 PHE cc_start: 0.7974 (m-80) cc_final: 0.6685 (t80) REVERT: A 392 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7105 (m-80) REVERT: A 422 ASN cc_start: 0.4199 (OUTLIER) cc_final: 0.3991 (p0) REVERT: A 434 ILE cc_start: 0.8637 (mp) cc_final: 0.7907 (tp) REVERT: A 453 TYR cc_start: 0.7201 (p90) cc_final: 0.6692 (p90) REVERT: A 574 ASP cc_start: 0.8029 (t0) cc_final: 0.7690 (t0) REVERT: A 985 ASP cc_start: 0.8124 (p0) cc_final: 0.7593 (p0) REVERT: A 988 GLU cc_start: 0.8297 (mp0) cc_final: 0.7935 (mp0) REVERT: B 100 ILE cc_start: 0.7780 (mm) cc_final: 0.7475 (mm) REVERT: B 133 PHE cc_start: 0.7595 (m-80) cc_final: 0.6523 (t80) REVERT: B 420 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6783 (m-30) REVERT: B 434 ILE cc_start: 0.8840 (mt) cc_final: 0.8187 (tp) REVERT: B 453 TYR cc_start: 0.7353 (p90) cc_final: 0.6878 (p90) REVERT: B 574 ASP cc_start: 0.7844 (t0) cc_final: 0.7311 (t0) REVERT: B 985 ASP cc_start: 0.8222 (p0) cc_final: 0.7653 (p0) REVERT: B 988 GLU cc_start: 0.8335 (mp0) cc_final: 0.8081 (mp0) REVERT: B 1004 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8975 (tt) REVERT: B 1029 MET cc_start: 0.8824 (tpp) cc_final: 0.8451 (tpp) REVERT: C 100 ILE cc_start: 0.7813 (mm) cc_final: 0.7473 (mm) REVERT: C 104 TRP cc_start: 0.8032 (m-90) cc_final: 0.7738 (m-90) REVERT: C 133 PHE cc_start: 0.7607 (m-80) cc_final: 0.7212 (m-80) REVERT: C 231 ILE cc_start: 0.9017 (mm) cc_final: 0.8594 (mt) REVERT: C 383 SER cc_start: 0.8696 (m) cc_final: 0.8406 (p) REVERT: C 389 ASP cc_start: 0.7676 (t0) cc_final: 0.7338 (t0) REVERT: C 422 ASN cc_start: 0.4529 (OUTLIER) cc_final: 0.3935 (p0) REVERT: C 574 ASP cc_start: 0.7945 (t70) cc_final: 0.7485 (t0) outliers start: 71 outliers final: 45 residues processed: 204 average time/residue: 0.1320 time to fit residues: 45.1260 Evaluate side-chains 175 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 224 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 274 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 239 optimal weight: 0.5980 chunk 272 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 110 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 214 optimal weight: 0.5980 chunk 26 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN B 540 ASN B 764 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.127285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.092550 restraints weight = 39321.062| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.56 r_work: 0.3293 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23340 Z= 0.120 Angle : 0.509 7.625 31776 Z= 0.268 Chirality : 0.043 0.161 3636 Planarity : 0.004 0.042 4095 Dihedral : 6.100 52.444 3153 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.43 % Allowed : 8.53 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.16), residues: 2841 helix: 1.72 (0.21), residues: 657 sheet: -0.18 (0.19), residues: 660 loop : -0.54 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.017 0.001 TYR C1067 PHE 0.024 0.001 PHE B 140 TRP 0.026 0.001 TRP B 104 HIS 0.007 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00277 (23304) covalent geometry : angle 0.50664 (31704) SS BOND : bond 0.00184 ( 36) SS BOND : angle 1.13361 ( 72) hydrogen bonds : bond 0.03365 ( 1006) hydrogen bonds : angle 5.30601 ( 2829) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 126 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7932 (m-90) cc_final: 0.7429 (m-90) REVERT: A 133 PHE cc_start: 0.7916 (m-80) cc_final: 0.6706 (t80) REVERT: A 392 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7169 (m-80) REVERT: A 453 TYR cc_start: 0.7194 (p90) cc_final: 0.6689 (p90) REVERT: A 574 ASP cc_start: 0.7989 (t0) cc_final: 0.7623 (t0) REVERT: A 985 ASP cc_start: 0.8081 (p0) cc_final: 0.7836 (p0) REVERT: A 990 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7638 (mp0) REVERT: B 133 PHE cc_start: 0.7693 (m-80) cc_final: 0.6592 (t80) REVERT: B 421 TYR cc_start: 0.4169 (OUTLIER) cc_final: 0.3853 (m-80) REVERT: B 434 ILE cc_start: 0.8872 (mt) cc_final: 0.8178 (tp) REVERT: B 453 TYR cc_start: 0.7156 (p90) cc_final: 0.6738 (p90) REVERT: B 574 ASP cc_start: 0.7900 (t0) cc_final: 0.7354 (t0) REVERT: B 985 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7950 (p0) REVERT: B 988 GLU cc_start: 0.8434 (mp0) cc_final: 0.8162 (pm20) REVERT: B 1004 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8962 (tt) REVERT: B 1029 MET cc_start: 0.8842 (tpp) cc_final: 0.8468 (tpp) REVERT: C 133 PHE cc_start: 0.7567 (m-80) cc_final: 0.6521 (t80) REVERT: C 231 ILE cc_start: 0.9053 (mm) cc_final: 0.8654 (mt) REVERT: C 574 ASP cc_start: 0.8026 (t70) cc_final: 0.7498 (t0) REVERT: C 1106 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8219 (pt0) outliers start: 62 outliers final: 40 residues processed: 178 average time/residue: 0.1373 time to fit residues: 41.0126 Evaluate side-chains 159 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 177 optimal weight: 4.9990 chunk 241 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 chunk 176 optimal weight: 0.0370 chunk 93 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 289 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.125547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.093665 restraints weight = 39194.257| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.62 r_work: 0.3229 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23340 Z= 0.181 Angle : 0.523 8.118 31776 Z= 0.275 Chirality : 0.044 0.179 3636 Planarity : 0.004 0.043 4095 Dihedral : 5.976 52.963 3150 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.82 % Allowed : 8.84 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.16), residues: 2841 helix: 1.87 (0.21), residues: 657 sheet: -0.09 (0.20), residues: 651 loop : -0.63 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 567 TYR 0.018 0.001 TYR C1067 PHE 0.016 0.002 PHE C1089 TRP 0.022 0.001 TRP B 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00429 (23304) covalent geometry : angle 0.52115 (31704) SS BOND : bond 0.00209 ( 36) SS BOND : angle 1.12602 ( 72) hydrogen bonds : bond 0.03480 ( 1006) hydrogen bonds : angle 5.30296 ( 2829) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 121 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7969 (m-90) cc_final: 0.7518 (m-90) REVERT: A 133 PHE cc_start: 0.7964 (m-80) cc_final: 0.6721 (t80) REVERT: A 392 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: A 422 ASN cc_start: 0.4266 (OUTLIER) cc_final: 0.4033 (p0) REVERT: A 453 TYR cc_start: 0.7241 (p90) cc_final: 0.6777 (p90) REVERT: A 574 ASP cc_start: 0.8212 (t0) cc_final: 0.7847 (t0) REVERT: A 990 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7747 (mp0) REVERT: B 133 PHE cc_start: 0.7787 (m-80) cc_final: 0.6675 (t80) REVERT: B 389 ASP cc_start: 0.7901 (t0) cc_final: 0.7630 (t0) REVERT: B 421 TYR cc_start: 0.4318 (OUTLIER) cc_final: 0.3859 (m-80) REVERT: B 434 ILE cc_start: 0.8950 (mt) cc_final: 0.8223 (tp) REVERT: B 453 TYR cc_start: 0.7195 (p90) cc_final: 0.6793 (p90) REVERT: B 574 ASP cc_start: 0.8066 (t0) cc_final: 0.7618 (t0) REVERT: B 985 ASP cc_start: 0.8346 (p0) cc_final: 0.8123 (p0) REVERT: B 1004 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9010 (tt) REVERT: B 1029 MET cc_start: 0.8930 (tpp) cc_final: 0.8596 (tpp) REVERT: C 117 LEU cc_start: 0.7547 (tp) cc_final: 0.7214 (mt) REVERT: C 133 PHE cc_start: 0.7736 (m-80) cc_final: 0.6705 (t80) REVERT: C 383 SER cc_start: 0.8745 (m) cc_final: 0.8520 (p) REVERT: C 574 ASP cc_start: 0.8090 (t70) cc_final: 0.7610 (t0) REVERT: C 1106 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8318 (pt0) outliers start: 72 outliers final: 51 residues processed: 184 average time/residue: 0.1383 time to fit residues: 42.7975 Evaluate side-chains 170 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 114 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 71 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 83 optimal weight: 0.5980 chunk 250 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.125488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.093849 restraints weight = 39271.758| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.68 r_work: 0.3223 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23340 Z= 0.171 Angle : 0.512 7.857 31776 Z= 0.269 Chirality : 0.044 0.168 3636 Planarity : 0.004 0.042 4095 Dihedral : 5.842 52.621 3147 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.09 % Allowed : 8.65 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.16), residues: 2841 helix: 2.04 (0.21), residues: 657 sheet: -0.14 (0.20), residues: 651 loop : -0.65 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.018 0.001 TYR C1067 PHE 0.019 0.001 PHE C 140 TRP 0.024 0.001 TRP B 104 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00405 (23304) covalent geometry : angle 0.50970 (31704) SS BOND : bond 0.00208 ( 36) SS BOND : angle 1.09586 ( 72) hydrogen bonds : bond 0.03377 ( 1006) hydrogen bonds : angle 5.25418 ( 2829) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 119 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7887 (m-90) cc_final: 0.7412 (m-90) REVERT: A 133 PHE cc_start: 0.7865 (m-80) cc_final: 0.6681 (t80) REVERT: A 392 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7493 (m-80) REVERT: A 422 ASN cc_start: 0.4432 (OUTLIER) cc_final: 0.4223 (p0) REVERT: A 453 TYR cc_start: 0.7252 (p90) cc_final: 0.6798 (p90) REVERT: A 574 ASP cc_start: 0.8057 (t0) cc_final: 0.7682 (t0) REVERT: A 990 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7565 (mp0) REVERT: B 84 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7935 (mp) REVERT: B 133 PHE cc_start: 0.7773 (m-80) cc_final: 0.6736 (t80) REVERT: B 226 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8190 (tp) REVERT: B 389 ASP cc_start: 0.7901 (t0) cc_final: 0.7651 (t0) REVERT: B 421 TYR cc_start: 0.4291 (OUTLIER) cc_final: 0.3940 (m-80) REVERT: B 434 ILE cc_start: 0.8879 (mt) cc_final: 0.8144 (tp) REVERT: B 453 TYR cc_start: 0.7256 (p90) cc_final: 0.6913 (p90) REVERT: B 574 ASP cc_start: 0.7857 (t0) cc_final: 0.7327 (t0) REVERT: B 900 MET cc_start: 0.8413 (mtp) cc_final: 0.8144 (mtm) REVERT: B 1004 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8885 (tt) REVERT: B 1029 MET cc_start: 0.8786 (tpp) cc_final: 0.8485 (tpp) REVERT: C 117 LEU cc_start: 0.7438 (tp) cc_final: 0.7141 (mt) REVERT: C 133 PHE cc_start: 0.7725 (m-80) cc_final: 0.6725 (t80) REVERT: C 383 SER cc_start: 0.8673 (m) cc_final: 0.8400 (p) REVERT: C 574 ASP cc_start: 0.7939 (t70) cc_final: 0.7476 (t0) REVERT: C 1106 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8239 (pt0) outliers start: 79 outliers final: 54 residues processed: 192 average time/residue: 0.1331 time to fit residues: 42.9720 Evaluate side-chains 173 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 112 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 64 optimal weight: 0.3980 chunk 261 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 117 optimal weight: 0.0050 chunk 63 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 277 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.127153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.093217 restraints weight = 39240.403| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.57 r_work: 0.3283 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23340 Z= 0.110 Angle : 0.478 8.557 31776 Z= 0.252 Chirality : 0.043 0.161 3636 Planarity : 0.004 0.041 4095 Dihedral : 5.564 52.593 3145 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.54 % Allowed : 9.08 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.16), residues: 2841 helix: 2.26 (0.21), residues: 657 sheet: -0.09 (0.20), residues: 645 loop : -0.56 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.017 0.001 TYR A1067 PHE 0.014 0.001 PHE B 347 TRP 0.027 0.001 TRP B 104 HIS 0.002 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00249 (23304) covalent geometry : angle 0.47649 (31704) SS BOND : bond 0.00304 ( 36) SS BOND : angle 0.86097 ( 72) hydrogen bonds : bond 0.03129 ( 1006) hydrogen bonds : angle 5.09911 ( 2829) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 127 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7949 (m-90) cc_final: 0.7501 (m-90) REVERT: A 133 PHE cc_start: 0.7941 (m-80) cc_final: 0.6825 (t80) REVERT: A 392 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: A 422 ASN cc_start: 0.4552 (OUTLIER) cc_final: 0.4345 (p0) REVERT: A 453 TYR cc_start: 0.7213 (p90) cc_final: 0.6772 (p90) REVERT: A 574 ASP cc_start: 0.8151 (t0) cc_final: 0.7769 (t0) REVERT: A 985 ASP cc_start: 0.7973 (p0) cc_final: 0.7731 (p0) REVERT: A 990 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7682 (mp0) REVERT: B 133 PHE cc_start: 0.7553 (m-80) cc_final: 0.6782 (t80) REVERT: B 226 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8084 (tp) REVERT: B 421 TYR cc_start: 0.4569 (OUTLIER) cc_final: 0.3889 (m-80) REVERT: B 434 ILE cc_start: 0.8796 (mt) cc_final: 0.8033 (tp) REVERT: B 453 TYR cc_start: 0.7185 (p90) cc_final: 0.6828 (p90) REVERT: B 574 ASP cc_start: 0.7948 (t0) cc_final: 0.7400 (t0) REVERT: B 900 MET cc_start: 0.8575 (mtp) cc_final: 0.8279 (mtm) REVERT: B 1004 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8877 (tt) REVERT: B 1029 MET cc_start: 0.8865 (tpp) cc_final: 0.8590 (tpp) REVERT: C 117 LEU cc_start: 0.7413 (tp) cc_final: 0.7111 (mt) REVERT: C 133 PHE cc_start: 0.7693 (m-80) cc_final: 0.6742 (t80) REVERT: C 383 SER cc_start: 0.8678 (m) cc_final: 0.8397 (p) REVERT: C 574 ASP cc_start: 0.8042 (t70) cc_final: 0.7554 (t0) REVERT: C 900 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8309 (mtp) REVERT: C 990 GLU cc_start: 0.7981 (mp0) cc_final: 0.7633 (mp0) REVERT: C 1106 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8165 (pt0) outliers start: 65 outliers final: 46 residues processed: 185 average time/residue: 0.1393 time to fit residues: 43.1888 Evaluate side-chains 162 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 109 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 217 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 210 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 204 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 187 optimal weight: 0.4980 chunk 275 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.127314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.094935 restraints weight = 38964.410| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.54 r_work: 0.3286 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23340 Z= 0.114 Angle : 0.478 8.354 31776 Z= 0.252 Chirality : 0.043 0.153 3636 Planarity : 0.004 0.042 4095 Dihedral : 5.421 52.758 3143 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.39 % Allowed : 9.55 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.16), residues: 2841 helix: 2.32 (0.21), residues: 660 sheet: -0.13 (0.20), residues: 639 loop : -0.51 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.017 0.001 TYR C1067 PHE 0.019 0.001 PHE C 140 TRP 0.023 0.001 TRP B 104 HIS 0.002 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00263 (23304) covalent geometry : angle 0.47582 (31704) SS BOND : bond 0.00169 ( 36) SS BOND : angle 1.08163 ( 72) hydrogen bonds : bond 0.03072 ( 1006) hydrogen bonds : angle 5.01880 ( 2829) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 127 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7932 (m-90) cc_final: 0.7559 (m-90) REVERT: A 133 PHE cc_start: 0.7824 (m-80) cc_final: 0.6814 (t80) REVERT: A 392 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7599 (m-80) REVERT: A 453 TYR cc_start: 0.7189 (p90) cc_final: 0.6730 (p90) REVERT: A 574 ASP cc_start: 0.8115 (t0) cc_final: 0.7784 (t0) REVERT: A 985 ASP cc_start: 0.8039 (p0) cc_final: 0.7746 (p0) REVERT: A 990 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7684 (mp0) REVERT: B 133 PHE cc_start: 0.7450 (m-80) cc_final: 0.6665 (t80) REVERT: B 226 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8276 (tp) REVERT: B 377 PHE cc_start: 0.7989 (t80) cc_final: 0.7616 (t80) REVERT: B 421 TYR cc_start: 0.4590 (OUTLIER) cc_final: 0.3875 (m-80) REVERT: B 434 ILE cc_start: 0.8801 (mt) cc_final: 0.8042 (tp) REVERT: B 453 TYR cc_start: 0.7104 (p90) cc_final: 0.6754 (p90) REVERT: B 574 ASP cc_start: 0.7975 (t0) cc_final: 0.7436 (t0) REVERT: B 1004 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8876 (tt) REVERT: B 1029 MET cc_start: 0.8865 (tpp) cc_final: 0.8626 (tpp) REVERT: C 117 LEU cc_start: 0.7438 (tp) cc_final: 0.7144 (mt) REVERT: C 133 PHE cc_start: 0.7485 (m-80) cc_final: 0.6734 (t80) REVERT: C 383 SER cc_start: 0.8678 (m) cc_final: 0.8422 (p) REVERT: C 574 ASP cc_start: 0.8071 (t70) cc_final: 0.7567 (t0) REVERT: C 900 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8264 (mtp) REVERT: C 990 GLU cc_start: 0.8086 (mp0) cc_final: 0.7832 (mp0) REVERT: C 1106 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8145 (pt0) outliers start: 61 outliers final: 49 residues processed: 179 average time/residue: 0.1342 time to fit residues: 40.3843 Evaluate side-chains 171 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 116 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 223 optimal weight: 0.0570 chunk 105 optimal weight: 0.0270 chunk 18 optimal weight: 0.9980 chunk 175 optimal weight: 0.6980 chunk 239 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 244 optimal weight: 0.5980 chunk 132 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.128842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.097069 restraints weight = 39248.632| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.62 r_work: 0.3305 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23340 Z= 0.093 Angle : 0.465 8.739 31776 Z= 0.245 Chirality : 0.042 0.146 3636 Planarity : 0.004 0.043 4095 Dihedral : 5.231 52.799 3143 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.11 % Allowed : 9.82 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.16), residues: 2841 helix: 2.46 (0.21), residues: 660 sheet: -0.14 (0.20), residues: 633 loop : -0.41 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.016 0.001 TYR B1067 PHE 0.018 0.001 PHE C 65 TRP 0.023 0.001 TRP B 104 HIS 0.003 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00206 (23304) covalent geometry : angle 0.46365 (31704) SS BOND : bond 0.00141 ( 36) SS BOND : angle 0.84223 ( 72) hydrogen bonds : bond 0.02906 ( 1006) hydrogen bonds : angle 4.85265 ( 2829) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 130 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8382 (t60) cc_final: 0.8149 (t60) REVERT: A 104 TRP cc_start: 0.7862 (m-90) cc_final: 0.7546 (m-90) REVERT: A 133 PHE cc_start: 0.7652 (m-80) cc_final: 0.6804 (t80) REVERT: A 392 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: A 422 ASN cc_start: 0.4952 (OUTLIER) cc_final: 0.4408 (p0) REVERT: A 453 TYR cc_start: 0.7039 (p90) cc_final: 0.6599 (p90) REVERT: A 574 ASP cc_start: 0.8112 (t0) cc_final: 0.7779 (t0) REVERT: A 581 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8098 (p) REVERT: A 990 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7698 (mp0) REVERT: B 133 PHE cc_start: 0.7285 (m-80) cc_final: 0.6665 (t80) REVERT: B 205 SER cc_start: 0.8777 (t) cc_final: 0.8470 (p) REVERT: B 421 TYR cc_start: 0.4674 (OUTLIER) cc_final: 0.3921 (m-80) REVERT: B 453 TYR cc_start: 0.7140 (p90) cc_final: 0.6759 (p90) REVERT: B 574 ASP cc_start: 0.7949 (t0) cc_final: 0.7415 (t0) REVERT: B 1004 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8852 (tt) REVERT: B 1029 MET cc_start: 0.8844 (tpp) cc_final: 0.8644 (tpp) REVERT: C 133 PHE cc_start: 0.7420 (m-80) cc_final: 0.6746 (t80) REVERT: C 383 SER cc_start: 0.8576 (m) cc_final: 0.8284 (p) REVERT: C 574 ASP cc_start: 0.8034 (t70) cc_final: 0.7586 (t0) REVERT: C 900 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8198 (mtp) REVERT: C 990 GLU cc_start: 0.8039 (mp0) cc_final: 0.7753 (mp0) outliers start: 54 outliers final: 44 residues processed: 173 average time/residue: 0.1331 time to fit residues: 38.5755 Evaluate side-chains 169 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 13 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 152 optimal weight: 5.9990 chunk 231 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 277 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.124595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.092961 restraints weight = 39488.174| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.64 r_work: 0.3196 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 23340 Z= 0.250 Angle : 0.559 9.732 31776 Z= 0.292 Chirality : 0.046 0.189 3636 Planarity : 0.004 0.046 4095 Dihedral : 5.570 53.077 3143 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.31 % Allowed : 9.82 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.16), residues: 2841 helix: 2.08 (0.20), residues: 666 sheet: -0.26 (0.20), residues: 639 loop : -0.55 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.020 0.001 TYR C1067 PHE 0.022 0.002 PHE A1121 TRP 0.013 0.001 TRP C 104 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00596 (23304) covalent geometry : angle 0.55642 (31704) SS BOND : bond 0.00288 ( 36) SS BOND : angle 1.15386 ( 72) hydrogen bonds : bond 0.03475 ( 1006) hydrogen bonds : angle 5.19846 ( 2829) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 121 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7919 (m-90) cc_final: 0.7489 (m-90) REVERT: A 133 PHE cc_start: 0.7686 (m-80) cc_final: 0.6846 (t80) REVERT: A 392 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: A 422 ASN cc_start: 0.4969 (OUTLIER) cc_final: 0.4424 (p0) REVERT: A 453 TYR cc_start: 0.7023 (p90) cc_final: 0.6579 (p90) REVERT: A 574 ASP cc_start: 0.8041 (t0) cc_final: 0.7720 (t0) REVERT: A 990 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7627 (mp0) REVERT: B 84 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7964 (mp) REVERT: B 133 PHE cc_start: 0.7318 (m-80) cc_final: 0.6698 (t80) REVERT: B 226 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8202 (tp) REVERT: B 377 PHE cc_start: 0.8097 (t80) cc_final: 0.7761 (t80) REVERT: B 421 TYR cc_start: 0.4568 (OUTLIER) cc_final: 0.3881 (m-80) REVERT: B 434 ILE cc_start: 0.8680 (mp) cc_final: 0.7934 (tp) REVERT: B 453 TYR cc_start: 0.7136 (p90) cc_final: 0.6795 (p90) REVERT: B 574 ASP cc_start: 0.7937 (t0) cc_final: 0.7486 (t0) REVERT: B 900 MET cc_start: 0.8442 (mtp) cc_final: 0.8182 (mtm) REVERT: B 1004 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8912 (tt) REVERT: B 1029 MET cc_start: 0.8834 (tpp) cc_final: 0.8592 (tpp) REVERT: C 133 PHE cc_start: 0.7573 (m-80) cc_final: 0.6851 (t80) REVERT: C 574 ASP cc_start: 0.8043 (t70) cc_final: 0.7566 (t0) REVERT: C 900 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8273 (mtp) REVERT: C 990 GLU cc_start: 0.7908 (mp0) cc_final: 0.7702 (mp0) REVERT: C 1106 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8269 (pt0) outliers start: 59 outliers final: 47 residues processed: 171 average time/residue: 0.1413 time to fit residues: 40.4727 Evaluate side-chains 170 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 115 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 143 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 202 optimal weight: 9.9990 chunk 72 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.126377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094735 restraints weight = 39350.827| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.70 r_work: 0.3227 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23340 Z= 0.142 Angle : 0.501 10.042 31776 Z= 0.261 Chirality : 0.044 0.170 3636 Planarity : 0.004 0.044 4095 Dihedral : 5.437 52.459 3143 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.19 % Allowed : 10.13 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 2841 helix: 2.26 (0.21), residues: 663 sheet: -0.38 (0.19), residues: 669 loop : -0.52 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.016 0.001 TYR C1067 PHE 0.019 0.001 PHE C 140 TRP 0.031 0.001 TRP B 104 HIS 0.002 0.000 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00333 (23304) covalent geometry : angle 0.49934 (31704) SS BOND : bond 0.00187 ( 36) SS BOND : angle 0.97439 ( 72) hydrogen bonds : bond 0.03161 ( 1006) hydrogen bonds : angle 5.07561 ( 2829) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5598.11 seconds wall clock time: 96 minutes 23.73 seconds (5783.73 seconds total)