Starting phenix.real_space_refine on Thu Jun 19 20:36:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x2c_22001/06_2025/6x2c_22001_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x2c_22001/06_2025/6x2c_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_22001/06_2025/6x2c_22001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x2c_22001/06_2025/6x2c_22001.map" model { file = "/net/cci-nas-00/data/ceres_data/6x2c_22001/06_2025/6x2c_22001_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x2c_22001/06_2025/6x2c_22001_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.68, per 1000 atoms: 0.64 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: 7.11 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 5.05 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: 13.47 Time building geometry restraints manager: 8.19 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: 0.27 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 15.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.670 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 63.810 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.800 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (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 TRP 0.069 0.018 TRP C1102 HIS 0.011 0.003 HIS B1058 PHE 0.070 0.011 PHE C 718 TYR 0.135 0.022 TYR B 423 ARG 0.011 0.002 ARG C1107 Details of bonding type rmsd hydrogen bonds : bond 0.16442 ( 1006) hydrogen bonds : angle 8.83494 ( 2829) SS BOND : bond 0.01090 ( 36) SS BOND : angle 1.94139 ( 72) covalent geometry : bond 0.01264 (23304) covalent geometry : angle 1.80790 (31704) *********************** 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 : 3.673 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: 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: 0.7434 (m-80) REVERT: A 574 ASP cc_start: 0.7396 (t0) cc_final: 0.7158 (t0) REVERT: B 64 TRP cc_start: 0.7874 (t60) cc_final: 0.7573 (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: 0.7883 (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: 0.7192 (t0) REVERT: B 1004 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8842 (tt) REVERT: C 64 TRP cc_start: 0.7752 (t60) cc_final: 0.7471 (t60) REVERT: C 574 ASP cc_start: 0.7353 (t0) cc_final: 0.7127 (t0) outliers start: 81 outliers final: 38 residues processed: 317 average time/residue: 0.4416 time to fit residues: 218.5730 Evaluate side-chains 178 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 2.857 ------------------------------------------------------------------------------- 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 245 optimal weight: 0.9990 chunk 220 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 117 optimal weight: 0.3980 chunk 228 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 264 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.137788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.100625 restraints weight = 41277.634| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.71 r_work: 0.3368 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23340 Z= 0.132 Angle : 0.593 7.746 31776 Z= 0.318 Chirality : 0.045 0.169 3636 Planarity : 0.004 0.040 4095 Dihedral : 7.350 59.137 3166 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.66 % Allowed : 7.16 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 2841 helix: 0.74 (0.20), residues: 639 sheet: -0.11 (0.19), residues: 642 loop : -0.67 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 64 HIS 0.002 0.000 HIS B1048 PHE 0.021 0.002 PHE C 140 TYR 0.017 0.001 TYR A1067 ARG 0.007 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 1006) hydrogen bonds : angle 5.94335 ( 2829) SS BOND : bond 0.00224 ( 36) SS BOND : angle 0.73428 ( 72) covalent geometry : bond 0.00287 (23304) covalent geometry : angle 0.59258 (31704) *********************** 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 233 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 165 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7749 (m-90) cc_final: 0.7407 (m-90) REVERT: A 133 PHE cc_start: 0.7877 (m-80) cc_final: 0.7419 (m-80) REVERT: A 378 LYS cc_start: 0.8334 (ttmm) cc_final: 0.8131 (ttmm) REVERT: A 392 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7108 (m-80) REVERT: A 574 ASP cc_start: 0.8059 (t0) cc_final: 0.7736 (t0) REVERT: A 985 ASP cc_start: 0.7912 (p0) cc_final: 0.6838 (p0) REVERT: B 133 PHE cc_start: 0.7790 (m-80) cc_final: 0.6358 (t80) REVERT: B 226 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8366 (tp) REVERT: B 353 TRP cc_start: 0.7808 (p-90) cc_final: 0.7341 (p-90) REVERT: B 434 ILE cc_start: 0.8756 (mt) cc_final: 0.8114 (tp) REVERT: B 574 ASP cc_start: 0.8092 (t0) cc_final: 0.7570 (t0) REVERT: B 869 MET cc_start: 0.9168 (mtt) cc_final: 0.8901 (mtp) REVERT: B 985 ASP cc_start: 0.8054 (p0) cc_final: 0.7115 (p0) REVERT: B 1004 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8997 (tt) REVERT: C 104 TRP cc_start: 0.7839 (m-90) cc_final: 0.7382 (m-90) REVERT: C 389 ASP cc_start: 0.7561 (t0) cc_final: 0.7321 (t0) REVERT: C 574 ASP cc_start: 0.7964 (t70) cc_final: 0.7487 (t0) outliers start: 68 outliers final: 42 residues processed: 216 average time/residue: 0.3492 time to fit residues: 119.3959 Evaluate side-chains 171 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 2.577 ------------------------------------------------------------------------------- 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 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 1094 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 248 optimal weight: 8.9990 chunk 161 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 237 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 ASN C 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.128542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.093865 restraints weight = 38851.176| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.56 r_work: 0.3310 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23340 Z= 0.119 Angle : 0.522 7.509 31776 Z= 0.277 Chirality : 0.044 0.162 3636 Planarity : 0.004 0.042 4095 Dihedral : 6.425 57.161 3159 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.46 % Allowed : 7.90 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2841 helix: 1.57 (0.21), residues: 636 sheet: -0.03 (0.19), residues: 642 loop : -0.55 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.002 0.000 HIS B1048 PHE 0.018 0.001 PHE B 347 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.000 ARG C 567 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 1006) hydrogen bonds : angle 5.42399 ( 2829) SS BOND : bond 0.00237 ( 36) SS BOND : angle 0.79065 ( 72) covalent geometry : bond 0.00268 (23304) covalent geometry : angle 0.52153 (31704) *********************** 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 204 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 141 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7896 (m-90) cc_final: 0.7425 (m-90) REVERT: A 133 PHE cc_start: 0.7939 (m-80) cc_final: 0.6676 (t80) REVERT: A 377 PHE cc_start: 0.7859 (t80) cc_final: 0.7616 (t80) REVERT: A 392 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7153 (m-80) REVERT: A 453 TYR cc_start: 0.7206 (p90) cc_final: 0.6662 (p90) REVERT: A 574 ASP cc_start: 0.8059 (t0) cc_final: 0.7665 (t0) REVERT: A 985 ASP cc_start: 0.8157 (p0) cc_final: 0.7603 (p0) REVERT: A 988 GLU cc_start: 0.8333 (mp0) cc_final: 0.8014 (mp0) REVERT: A 990 GLU cc_start: 0.8006 (mp0) cc_final: 0.7748 (mp0) REVERT: B 133 PHE cc_start: 0.7370 (m-80) cc_final: 0.6509 (t80) REVERT: B 434 ILE cc_start: 0.8832 (mt) cc_final: 0.8172 (tp) REVERT: B 453 TYR cc_start: 0.7334 (p90) cc_final: 0.6849 (p90) REVERT: B 574 ASP cc_start: 0.7909 (t70) cc_final: 0.7352 (t0) REVERT: B 584 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.7615 (mm) REVERT: B 985 ASP cc_start: 0.8226 (p0) cc_final: 0.7748 (p0) REVERT: B 988 GLU cc_start: 0.8457 (mp0) cc_final: 0.8140 (mp0) REVERT: B 1004 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8966 (tt) REVERT: B 1029 MET cc_start: 0.8850 (tpp) cc_final: 0.8465 (tpp) REVERT: C 133 PHE cc_start: 0.7822 (m-80) cc_final: 0.6299 (t80) REVERT: C 389 ASP cc_start: 0.7726 (t0) cc_final: 0.7352 (t0) REVERT: C 422 ASN cc_start: 0.4612 (OUTLIER) cc_final: 0.4382 (p0) REVERT: C 574 ASP cc_start: 0.8001 (t70) cc_final: 0.7537 (t0) outliers start: 63 outliers final: 37 residues processed: 193 average time/residue: 0.3063 time to fit residues: 99.7747 Evaluate side-chains 167 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 2.822 ------------------------------------------------------------------------------- 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 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 47 VAL 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 569 ILE 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 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 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 121 optimal weight: 9.9990 chunk 195 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 764 ASN B 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.122941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.091183 restraints weight = 39839.350| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.74 r_work: 0.3099 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 23340 Z= 0.324 Angle : 0.645 7.993 31776 Z= 0.337 Chirality : 0.049 0.210 3636 Planarity : 0.004 0.046 4095 Dihedral : 6.562 55.242 3153 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.93 % Allowed : 8.76 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 2841 helix: 1.27 (0.20), residues: 663 sheet: -0.22 (0.19), residues: 672 loop : -0.77 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 104 HIS 0.007 0.001 HIS C 245 PHE 0.026 0.002 PHE A1089 TYR 0.022 0.002 TYR B 170 ARG 0.004 0.001 ARG C 567 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 1006) hydrogen bonds : angle 5.68964 ( 2829) SS BOND : bond 0.00325 ( 36) SS BOND : angle 1.37908 ( 72) covalent geometry : bond 0.00779 (23304) covalent geometry : angle 0.64216 (31704) *********************** 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 211 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 136 time to evaluate : 2.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7989 (m-90) cc_final: 0.7511 (m-90) REVERT: A 133 PHE cc_start: 0.8021 (m-80) cc_final: 0.6761 (t80) REVERT: A 377 PHE cc_start: 0.7958 (t80) cc_final: 0.7735 (t80) REVERT: A 392 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7020 (m-80) REVERT: A 453 TYR cc_start: 0.7315 (p90) cc_final: 0.6865 (p90) REVERT: A 574 ASP cc_start: 0.8100 (t0) cc_final: 0.7729 (t0) REVERT: A 985 ASP cc_start: 0.8065 (p0) cc_final: 0.7679 (p0) REVERT: A 988 GLU cc_start: 0.8366 (mp0) cc_final: 0.8055 (mp0) REVERT: B 133 PHE cc_start: 0.7751 (m-80) cc_final: 0.6699 (t80) REVERT: B 389 ASP cc_start: 0.7732 (t0) cc_final: 0.7508 (t0) REVERT: B 421 TYR cc_start: 0.4133 (OUTLIER) cc_final: 0.3905 (m-80) REVERT: B 453 TYR cc_start: 0.7218 (p90) cc_final: 0.6881 (p90) REVERT: B 574 ASP cc_start: 0.7928 (t0) cc_final: 0.7482 (t0) REVERT: B 900 MET cc_start: 0.8477 (mtp) cc_final: 0.8255 (mtm) REVERT: B 988 GLU cc_start: 0.8368 (mp0) cc_final: 0.8120 (pm20) REVERT: B 1004 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9035 (tt) REVERT: B 1029 MET cc_start: 0.8906 (tpp) cc_final: 0.8545 (tpp) REVERT: C 100 ILE cc_start: 0.7956 (mm) cc_final: 0.7610 (mm) REVERT: C 133 PHE cc_start: 0.8078 (m-80) cc_final: 0.6712 (t80) REVERT: C 422 ASN cc_start: 0.4614 (OUTLIER) cc_final: 0.4394 (p0) REVERT: C 574 ASP cc_start: 0.7997 (t70) cc_final: 0.7515 (t0) REVERT: C 1106 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8404 (pt0) outliers start: 75 outliers final: 53 residues processed: 202 average time/residue: 0.2927 time to fit residues: 98.9301 Evaluate side-chains 178 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 120 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL 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 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 705 VAL 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 47 VAL 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 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 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 395 VAL 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 878 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 977 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 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 214 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 264 optimal weight: 0.8980 chunk 269 optimal weight: 0.7980 chunk 290 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 178 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN B 540 ASN B 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.126662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.094777 restraints weight = 39352.422| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.65 r_work: 0.3249 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23340 Z= 0.113 Angle : 0.498 8.178 31776 Z= 0.263 Chirality : 0.043 0.163 3636 Planarity : 0.004 0.042 4095 Dihedral : 5.970 51.967 3150 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.39 % Allowed : 9.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2841 helix: 1.98 (0.21), residues: 639 sheet: -0.35 (0.19), residues: 666 loop : -0.68 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 104 HIS 0.002 0.000 HIS A1048 PHE 0.016 0.001 PHE B 347 TYR 0.016 0.001 TYR A1067 ARG 0.006 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 1006) hydrogen bonds : angle 5.30466 ( 2829) SS BOND : bond 0.00187 ( 36) SS BOND : angle 0.72502 ( 72) covalent geometry : bond 0.00254 (23304) covalent geometry : angle 0.49747 (31704) *********************** 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 183 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 122 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7942 (m-90) cc_final: 0.7485 (m-90) REVERT: A 133 PHE cc_start: 0.7911 (m-80) cc_final: 0.6703 (t80) REVERT: A 392 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7253 (m-80) REVERT: A 453 TYR cc_start: 0.7200 (p90) cc_final: 0.6781 (p90) REVERT: A 574 ASP cc_start: 0.8036 (t0) cc_final: 0.7671 (t0) REVERT: A 985 ASP cc_start: 0.8067 (p0) cc_final: 0.7336 (p0) REVERT: A 988 GLU cc_start: 0.8403 (mp0) cc_final: 0.7865 (mp0) REVERT: B 133 PHE cc_start: 0.7785 (m-80) cc_final: 0.6714 (t80) REVERT: B 226 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8097 (tp) REVERT: B 421 TYR cc_start: 0.4347 (OUTLIER) cc_final: 0.3940 (m-80) REVERT: B 453 TYR cc_start: 0.7134 (p90) cc_final: 0.6765 (p90) REVERT: B 574 ASP cc_start: 0.7931 (t0) cc_final: 0.7427 (t0) REVERT: B 902 MET cc_start: 0.8588 (mmm) cc_final: 0.8367 (tpt) REVERT: B 985 ASP cc_start: 0.8307 (p0) cc_final: 0.8054 (p0) REVERT: B 990 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7634 (mp0) REVERT: B 1004 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8977 (tt) REVERT: B 1029 MET cc_start: 0.8865 (tpp) cc_final: 0.8525 (tpp) REVERT: C 133 PHE cc_start: 0.7745 (m-80) cc_final: 0.6749 (t80) REVERT: C 453 TYR cc_start: 0.7351 (p90) cc_final: 0.7031 (p90) REVERT: C 574 ASP cc_start: 0.8027 (t70) cc_final: 0.7562 (t0) outliers start: 61 outliers final: 41 residues processed: 175 average time/residue: 0.3111 time to fit residues: 91.1933 Evaluate side-chains 160 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 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 462 LYS Chi-restraints excluded: chain A residue 569 ILE 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 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 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 B residue 1106 GLN 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 383 SER Chi-restraints excluded: chain C residue 547 THR 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 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 115 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 288 optimal weight: 0.9980 chunk 80 optimal weight: 0.0970 chunk 157 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 422 ASN ** 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 = 0.3917 r_free = 0.3917 target = 0.124826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.092818 restraints weight = 39322.180| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.72 r_work: 0.3226 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23340 Z= 0.188 Angle : 0.519 7.828 31776 Z= 0.273 Chirality : 0.044 0.193 3636 Planarity : 0.004 0.042 4095 Dihedral : 5.918 52.611 3147 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.82 % Allowed : 9.43 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 2841 helix: 2.05 (0.21), residues: 657 sheet: -0.22 (0.20), residues: 660 loop : -0.75 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 104 HIS 0.004 0.001 HIS B1064 PHE 0.019 0.002 PHE C 140 TYR 0.018 0.001 TYR C1067 ARG 0.003 0.000 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 1006) hydrogen bonds : angle 5.29742 ( 2829) SS BOND : bond 0.00203 ( 36) SS BOND : angle 0.71724 ( 72) covalent geometry : bond 0.00446 (23304) covalent geometry : angle 0.51890 (31704) *********************** 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 192 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 120 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7933 (m-90) cc_final: 0.7492 (m-90) REVERT: A 133 PHE cc_start: 0.7864 (m-80) cc_final: 0.6716 (t80) REVERT: A 392 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7362 (m-80) REVERT: A 453 TYR cc_start: 0.7223 (p90) cc_final: 0.6816 (p90) REVERT: A 574 ASP cc_start: 0.8195 (t0) cc_final: 0.7830 (t0) REVERT: A 985 ASP cc_start: 0.8078 (p0) cc_final: 0.7810 (p0) REVERT: B 133 PHE cc_start: 0.7833 (m-80) cc_final: 0.6796 (t80) REVERT: B 226 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8261 (tp) REVERT: B 421 TYR cc_start: 0.4380 (OUTLIER) cc_final: 0.3921 (m-80) REVERT: B 453 TYR cc_start: 0.7238 (p90) cc_final: 0.6902 (p90) REVERT: B 574 ASP cc_start: 0.8026 (t0) cc_final: 0.7475 (t0) REVERT: B 900 MET cc_start: 0.8670 (mtp) cc_final: 0.8423 (mtm) REVERT: B 990 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7730 (mp0) REVERT: B 1004 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9002 (tt) REVERT: B 1029 MET cc_start: 0.8944 (tpp) cc_final: 0.8641 (tpp) REVERT: C 133 PHE cc_start: 0.7743 (m-80) cc_final: 0.6745 (t80) REVERT: C 453 TYR cc_start: 0.7368 (p90) cc_final: 0.7046 (p90) REVERT: C 574 ASP cc_start: 0.8075 (t70) cc_final: 0.7607 (t0) REVERT: C 1106 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8323 (pt0) outliers start: 72 outliers final: 49 residues processed: 182 average time/residue: 0.3171 time to fit residues: 96.9967 Evaluate side-chains 160 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 106 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 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 570 LEU Chi-restraints excluded: chain A residue 584 ILE 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 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 434 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 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 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 158 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 171 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 237 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 422 ASN ** 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 = 0.126473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.094772 restraints weight = 39661.111| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.75 r_work: 0.3248 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3214 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= 0.118 Angle : 0.483 8.365 31776 Z= 0.255 Chirality : 0.043 0.159 3636 Planarity : 0.004 0.042 4095 Dihedral : 5.703 52.376 3147 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.86 % Allowed : 9.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2841 helix: 2.29 (0.21), residues: 654 sheet: -0.26 (0.19), residues: 675 loop : -0.64 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 104 HIS 0.002 0.000 HIS B1048 PHE 0.015 0.001 PHE B 347 TYR 0.017 0.001 TYR A1067 ARG 0.003 0.000 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 1006) hydrogen bonds : angle 5.15311 ( 2829) SS BOND : bond 0.00155 ( 36) SS BOND : angle 0.78576 ( 72) covalent geometry : bond 0.00272 (23304) covalent geometry : angle 0.48169 (31704) *********************** 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 193 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 120 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7851 (m-90) cc_final: 0.7413 (m-90) REVERT: A 133 PHE cc_start: 0.7815 (m-80) cc_final: 0.6674 (t80) REVERT: A 392 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: A 453 TYR cc_start: 0.7221 (p90) cc_final: 0.6801 (p90) REVERT: A 574 ASP cc_start: 0.8028 (t0) cc_final: 0.7665 (t0) REVERT: A 985 ASP cc_start: 0.8059 (p0) cc_final: 0.7616 (p0) REVERT: A 988 GLU cc_start: 0.8191 (mp0) cc_final: 0.7838 (mp0) REVERT: A 990 GLU cc_start: 0.7758 (mp0) cc_final: 0.7505 (mp0) REVERT: B 133 PHE cc_start: 0.7703 (m-80) cc_final: 0.6699 (t80) REVERT: B 226 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8011 (tp) REVERT: B 421 TYR cc_start: 0.4431 (OUTLIER) cc_final: 0.3942 (m-80) REVERT: B 453 TYR cc_start: 0.7232 (p90) cc_final: 0.6858 (p90) REVERT: B 574 ASP cc_start: 0.7822 (t0) cc_final: 0.7303 (t0) REVERT: B 902 MET cc_start: 0.8377 (mmm) cc_final: 0.8146 (tpt) REVERT: B 1004 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8862 (tt) REVERT: B 1029 MET cc_start: 0.8741 (tpp) cc_final: 0.8448 (tpp) REVERT: C 133 PHE cc_start: 0.7648 (m-80) cc_final: 0.6677 (t80) REVERT: C 453 TYR cc_start: 0.7351 (p90) cc_final: 0.7019 (p90) REVERT: C 574 ASP cc_start: 0.7925 (t70) cc_final: 0.7481 (t0) outliers start: 73 outliers final: 50 residues processed: 184 average time/residue: 0.3290 time to fit residues: 101.6627 Evaluate side-chains 164 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 110 time to evaluate : 2.526 ------------------------------------------------------------------------------- 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 84 LEU 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 569 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 434 ILE 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 63 THR 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 383 SER Chi-restraints excluded: chain C residue 547 THR 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 36 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 164 optimal weight: 0.0570 chunk 21 optimal weight: 0.2980 chunk 210 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 422 ASN ** 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 = 0.3950 r_free = 0.3950 target = 0.127511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.096095 restraints weight = 39445.675| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.55 r_work: 0.3266 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23340 Z= 0.103 Angle : 0.467 8.569 31776 Z= 0.247 Chirality : 0.043 0.154 3636 Planarity : 0.004 0.042 4095 Dihedral : 5.407 52.451 3143 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.07 % Allowed : 10.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2841 helix: 2.37 (0.21), residues: 657 sheet: -0.22 (0.20), residues: 639 loop : -0.53 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 104 HIS 0.002 0.000 HIS B1048 PHE 0.018 0.001 PHE C 140 TYR 0.016 0.001 TYR A1067 ARG 0.003 0.000 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.03035 ( 1006) hydrogen bonds : angle 4.98366 ( 2829) SS BOND : bond 0.00155 ( 36) SS BOND : angle 0.64328 ( 72) covalent geometry : bond 0.00232 (23304) covalent geometry : angle 0.46647 (31704) *********************** 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 181 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 128 time to evaluate : 2.641 Fit side-chains revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7848 (m-90) cc_final: 0.7480 (m-90) REVERT: A 133 PHE cc_start: 0.7746 (m-80) cc_final: 0.6761 (t80) REVERT: A 392 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: A 453 TYR cc_start: 0.7125 (p90) cc_final: 0.6719 (p90) REVERT: A 574 ASP cc_start: 0.7965 (t0) cc_final: 0.7648 (t0) REVERT: A 985 ASP cc_start: 0.8084 (p0) cc_final: 0.7786 (p0) REVERT: A 988 GLU cc_start: 0.8248 (mp0) cc_final: 0.8033 (pm20) REVERT: B 133 PHE cc_start: 0.7421 (m-80) cc_final: 0.6624 (t80) REVERT: B 226 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8017 (tp) REVERT: B 377 PHE cc_start: 0.8033 (t80) cc_final: 0.7668 (t80) REVERT: B 434 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8050 (tp) REVERT: B 453 TYR cc_start: 0.7133 (p90) cc_final: 0.6776 (p90) REVERT: B 574 ASP cc_start: 0.7826 (t0) cc_final: 0.7317 (t0) REVERT: B 900 MET cc_start: 0.8294 (mtp) cc_final: 0.8005 (mtm) REVERT: B 902 MET cc_start: 0.8436 (mmm) cc_final: 0.8041 (tpt) REVERT: B 985 ASP cc_start: 0.8197 (p0) cc_final: 0.7948 (p0) REVERT: B 990 GLU cc_start: 0.7922 (mp0) cc_final: 0.7662 (mp0) REVERT: B 1004 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8818 (tt) REVERT: B 1029 MET cc_start: 0.8729 (tpp) cc_final: 0.8511 (tpp) REVERT: C 133 PHE cc_start: 0.7331 (m-80) cc_final: 0.6668 (t80) REVERT: C 453 TYR cc_start: 0.7312 (p90) cc_final: 0.6995 (p90) REVERT: C 574 ASP cc_start: 0.7956 (t70) cc_final: 0.7485 (t0) REVERT: C 985 ASP cc_start: 0.7806 (p0) cc_final: 0.6700 (p0) outliers start: 53 outliers final: 46 residues processed: 173 average time/residue: 0.3426 time to fit residues: 99.5908 Evaluate side-chains 163 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 113 time to evaluate : 2.825 ------------------------------------------------------------------------------- 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 84 LEU 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 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 434 ILE 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 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 63 THR 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 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 109 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 158 optimal weight: 0.8980 chunk 226 optimal weight: 6.9990 chunk 243 optimal weight: 0.0870 chunk 78 optimal weight: 0.5980 chunk 253 optimal weight: 3.9990 overall best weight: 1.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 422 ASN ** 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 = 0.3921 r_free = 0.3921 target = 0.125229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.093413 restraints weight = 39724.383| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.73 r_work: 0.3210 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23340 Z= 0.191 Angle : 0.516 7.904 31776 Z= 0.272 Chirality : 0.044 0.181 3636 Planarity : 0.004 0.043 4095 Dihedral : 5.553 52.665 3143 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.31 % Allowed : 10.21 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2841 helix: 2.17 (0.21), residues: 660 sheet: -0.34 (0.19), residues: 675 loop : -0.60 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 104 HIS 0.004 0.001 HIS B1064 PHE 0.022 0.002 PHE C 65 TYR 0.018 0.001 TYR C1067 ARG 0.002 0.000 ARG C 983 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 1006) hydrogen bonds : angle 5.14121 ( 2829) SS BOND : bond 0.00208 ( 36) SS BOND : angle 0.69296 ( 72) covalent geometry : bond 0.00453 (23304) covalent geometry : angle 0.51504 (31704) *********************** 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 174 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 115 time to evaluate : 2.573 Fit side-chains REVERT: A 104 TRP cc_start: 0.7876 (m-90) cc_final: 0.7445 (m-90) REVERT: A 133 PHE cc_start: 0.7704 (m-80) cc_final: 0.6832 (t80) REVERT: A 392 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7546 (m-80) REVERT: A 453 TYR cc_start: 0.7016 (p90) cc_final: 0.6586 (p90) REVERT: A 574 ASP cc_start: 0.8015 (t0) cc_final: 0.7697 (t0) REVERT: A 985 ASP cc_start: 0.8097 (p0) cc_final: 0.7629 (p0) REVERT: A 988 GLU cc_start: 0.8275 (mp0) cc_final: 0.7984 (mp0) REVERT: B 133 PHE cc_start: 0.7419 (m-80) cc_final: 0.6605 (t80) REVERT: B 226 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8184 (tp) REVERT: B 421 TYR cc_start: 0.4570 (OUTLIER) cc_final: 0.3961 (m-80) REVERT: B 453 TYR cc_start: 0.7131 (p90) cc_final: 0.6779 (p90) REVERT: B 574 ASP cc_start: 0.7903 (t0) cc_final: 0.7339 (t0) REVERT: B 900 MET cc_start: 0.8449 (mtp) cc_final: 0.8164 (mtm) REVERT: B 990 GLU cc_start: 0.7927 (mp0) cc_final: 0.7677 (mp0) REVERT: B 1004 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8903 (tt) REVERT: B 1029 MET cc_start: 0.8799 (tpp) cc_final: 0.8544 (tpp) REVERT: C 133 PHE cc_start: 0.7386 (m-80) cc_final: 0.6717 (t80) REVERT: C 453 TYR cc_start: 0.7305 (p90) cc_final: 0.6989 (p90) REVERT: C 574 ASP cc_start: 0.7976 (t70) cc_final: 0.7503 (t0) REVERT: C 985 ASP cc_start: 0.8060 (p0) cc_final: 0.7813 (p0) REVERT: C 990 GLU cc_start: 0.7812 (mp0) cc_final: 0.7606 (mp0) REVERT: C 1106 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8189 (pt0) outliers start: 59 outliers final: 47 residues processed: 166 average time/residue: 0.3148 time to fit residues: 87.4408 Evaluate side-chains 163 residues out of total 2556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 111 time to evaluate : 2.568 ------------------------------------------------------------------------------- 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 84 LEU 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 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 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 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 63 THR 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 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 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.6436 > 50: distance: 55 - 103: 33.903 distance: 58 - 100: 20.036 distance: 68 - 90: 26.086 distance: 82 - 87: 22.992 distance: 87 - 88: 6.722 distance: 88 - 89: 23.883 distance: 88 - 91: 13.667 distance: 89 - 90: 28.163 distance: 89 - 95: 17.488 distance: 91 - 92: 18.131 distance: 92 - 93: 10.206 distance: 92 - 94: 3.224 distance: 95 - 96: 21.893 distance: 96 - 97: 30.676 distance: 96 - 99: 42.837 distance: 97 - 98: 8.999 distance: 97 - 100: 24.964 distance: 100 - 101: 10.038 distance: 101 - 102: 19.420 distance: 101 - 104: 44.955 distance: 102 - 103: 46.308 distance: 102 - 107: 35.405 distance: 104 - 105: 21.908 distance: 104 - 106: 33.938 distance: 107 - 108: 25.059 distance: 108 - 109: 5.541 distance: 108 - 111: 30.243 distance: 109 - 110: 15.484 distance: 109 - 115: 32.711 distance: 111 - 112: 37.719 distance: 115 - 116: 26.422 distance: 116 - 117: 49.224 distance: 116 - 119: 17.146 distance: 117 - 118: 46.177 distance: 117 - 121: 44.212 distance: 119 - 120: 9.719 distance: 120 - 190: 26.171 distance: 121 - 122: 43.418 distance: 122 - 123: 38.353 distance: 122 - 125: 24.856 distance: 123 - 124: 29.413 distance: 123 - 126: 36.201 distance: 126 - 127: 8.845 distance: 127 - 128: 35.328 distance: 127 - 130: 10.895 distance: 128 - 129: 16.103 distance: 128 - 134: 30.539 distance: 130 - 131: 41.253 distance: 131 - 132: 22.135 distance: 131 - 133: 25.962 distance: 134 - 135: 31.953 distance: 135 - 136: 33.161 distance: 135 - 138: 27.983 distance: 136 - 137: 31.545 distance: 136 - 142: 23.468 distance: 137 - 163: 27.364 distance: 138 - 139: 17.063 distance: 139 - 140: 4.105 distance: 139 - 141: 37.190 distance: 142 - 143: 6.510 distance: 142 - 148: 34.356 distance: 143 - 144: 5.656 distance: 143 - 146: 14.457 distance: 144 - 145: 32.229 distance: 144 - 149: 17.048 distance: 145 - 172: 30.569 distance: 146 - 147: 16.745 distance: 147 - 148: 27.171 distance: 149 - 150: 5.403 distance: 150 - 151: 16.257 distance: 150 - 153: 11.281 distance: 151 - 152: 26.900 distance: 151 - 157: 17.040 distance: 152 - 179: 30.295 distance: 153 - 154: 34.949 distance: 154 - 155: 3.674 distance: 154 - 156: 16.908