Starting phenix.real_space_refine on Mon Sep 30 06:53:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmd_37650/09_2024/8wmd_37650_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmd_37650/09_2024/8wmd_37650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmd_37650/09_2024/8wmd_37650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmd_37650/09_2024/8wmd_37650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmd_37650/09_2024/8wmd_37650_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmd_37650/09_2024/8wmd_37650_neut.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 108 5.16 5 C 15594 2.51 5 N 4029 2.21 5 O 4698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24429 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 7989 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 54, 'TRANS': 966} Chain breaks: 7 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Restraints were copied for chains: C, B Time building chain proxies: 22.01, per 1000 atoms: 0.90 Number of scatterers: 24429 At special positions: 0 Unit cell: (133.665, 141.705, 166.83, 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 108 16.00 O 4698 8.00 N 4029 7.00 C 15594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " Time building additional restraints: 5.79 Conformation dependent library (CDL) restraints added in 2.9 seconds 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5748 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 42 sheets defined 24.1% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.779A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.046A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.430A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.709A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.883A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.543A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.069A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.621A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.866A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.674A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.289A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.779A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.047A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.430A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.709A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.883A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.543A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.069A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.621A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.866A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.674A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.289A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.779A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 4.046A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.430A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.709A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.883A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.543A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.069A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.622A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.866A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.674A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.289A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.636A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.874A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.339A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.076A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 325 through 327 removed outlier: 4.244A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.826A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=10, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.824A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.796A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.627A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=14, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=15, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.637A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.874A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=18, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.339A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.076A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'B' and resid 325 through 327 removed outlier: 4.244A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.825A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=23, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=24, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.824A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.796A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.627A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=28, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=29, first strand: chain 'C' and resid 25 through 30 removed outlier: 7.636A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.874A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=32, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.339A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.076A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'C' and resid 325 through 327 removed outlier: 4.244A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.826A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=37, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=38, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.824A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.795A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.628A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=42, first strand: chain 'C' and resid 1094 through 1097 963 hydrogen bonds defined for protein. 2619 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: 9.58 Time building geometry restraints manager: 6.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7725 1.34 - 1.46: 5643 1.46 - 1.58: 11487 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 24990 Sorted by residual: bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C1 NAG B1310 " pdb=" O5 NAG B1310 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.73e+00 bond pdb=" C1 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.66e+00 ... (remaining 24985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 33036 1.34 - 2.68: 770 2.68 - 4.02: 172 4.02 - 5.36: 18 5.36 - 6.70: 9 Bond angle restraints: 34005 Sorted by residual: angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.34 119.04 -6.70 2.04e+00 2.40e-01 1.08e+01 angle pdb=" N GLY A 526 " pdb=" CA GLY A 526 " pdb=" C GLY A 526 " ideal model delta sigma weight residual 112.34 119.03 -6.69 2.04e+00 2.40e-01 1.07e+01 angle pdb=" N GLY B 526 " pdb=" CA GLY B 526 " pdb=" C GLY B 526 " ideal model delta sigma weight residual 112.34 119.02 -6.68 2.04e+00 2.40e-01 1.07e+01 angle pdb=" N ASN A 282 " pdb=" CA ASN A 282 " pdb=" CB ASN A 282 " ideal model delta sigma weight residual 110.95 106.84 4.11 1.44e+00 4.82e-01 8.14e+00 angle pdb=" N ASN B 282 " pdb=" CA ASN B 282 " pdb=" CB ASN B 282 " ideal model delta sigma weight residual 110.95 106.86 4.09 1.44e+00 4.82e-01 8.07e+00 ... (remaining 34000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 14044 17.81 - 35.61: 998 35.61 - 53.42: 180 53.42 - 71.23: 30 71.23 - 89.04: 12 Dihedral angle restraints: 15264 sinusoidal: 6339 harmonic: 8925 Sorted by residual: dihedral pdb=" CA GLU C 281 " pdb=" C GLU C 281 " pdb=" N ASN C 282 " pdb=" CA ASN C 282 " ideal model delta harmonic sigma weight residual -180.00 -150.94 -29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA GLU B 281 " pdb=" C GLU B 281 " pdb=" N ASN B 282 " pdb=" CA ASN B 282 " ideal model delta harmonic sigma weight residual 180.00 -150.94 -29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA GLU A 281 " pdb=" C GLU A 281 " pdb=" N ASN A 282 " pdb=" CA ASN A 282 " ideal model delta harmonic sigma weight residual -180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 15261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 3954 0.188 - 0.375: 3 0.375 - 0.563: 0 0.563 - 0.750: 0 0.750 - 0.938: 3 Chirality restraints: 3960 Sorted by residual: chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.19e+01 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.19e+01 ... (remaining 3957 not shown) Planarity restraints: 4380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 282 " 0.041 2.00e-02 2.50e+03 3.73e-02 1.74e+01 pdb=" CG ASN A 282 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN A 282 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 282 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 282 " 0.041 2.00e-02 2.50e+03 3.73e-02 1.74e+01 pdb=" CG ASN B 282 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 282 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 282 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 282 " 0.041 2.00e-02 2.50e+03 3.73e-02 1.74e+01 pdb=" CG ASN C 282 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN C 282 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 282 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG C1305 " 0.042 2.00e-02 2.50e+03 ... (remaining 4377 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 203 2.60 - 3.18: 20174 3.18 - 3.75: 34903 3.75 - 4.33: 49049 4.33 - 4.90: 83611 Nonbonded interactions: 187940 Sorted by model distance: nonbonded pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " model vdw 2.030 3.760 ... (remaining 187935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.940 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 61.030 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.003 0.070 24990 Z= 0.188 Angle : 0.519 6.705 34005 Z= 0.273 Chirality : 0.050 0.938 3960 Planarity : 0.003 0.043 4347 Dihedral : 12.395 89.036 9477 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.34 % Allowed : 9.28 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.09 (0.15), residues: 3015 helix: 2.30 (0.21), residues: 630 sheet: 0.76 (0.20), residues: 687 loop : -1.18 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 886 HIS 0.002 0.001 HIS B 52 PHE 0.008 0.001 PHE A 400 TYR 0.014 0.001 TYR B1067 ARG 0.004 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 287 time to evaluate : 2.811 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.6755 (p90) cc_final: 0.6522 (p90) REVERT: A 237 ARG cc_start: 0.7905 (mtm180) cc_final: 0.6906 (mtm110) REVERT: A 309 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7803 (mp0) REVERT: A 794 ILE cc_start: 0.8319 (tt) cc_final: 0.8079 (pp) REVERT: A 1050 MET cc_start: 0.9384 (ptm) cc_final: 0.9165 (ptm) REVERT: B 121 ASN cc_start: 0.8424 (m-40) cc_final: 0.8212 (t0) REVERT: B 140 PHE cc_start: 0.6859 (p90) cc_final: 0.6596 (p90) REVERT: B 237 ARG cc_start: 0.7874 (mtm180) cc_final: 0.7010 (mtm110) REVERT: B 309 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8070 (mp0) REVERT: C 121 ASN cc_start: 0.8574 (m-40) cc_final: 0.8287 (t0) REVERT: C 140 PHE cc_start: 0.6543 (p90) cc_final: 0.6241 (p90) REVERT: C 160 TYR cc_start: 0.8170 (p90) cc_final: 0.7967 (p90) REVERT: C 220 PHE cc_start: 0.7363 (m-80) cc_final: 0.7042 (m-80) REVERT: C 237 ARG cc_start: 0.7864 (mtm180) cc_final: 0.7046 (mtm110) REVERT: C 309 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7681 (mp0) REVERT: C 1038 LYS cc_start: 0.8974 (mttp) cc_final: 0.8709 (mmtp) outliers start: 9 outliers final: 8 residues processed: 296 average time/residue: 1.1087 time to fit residues: 390.9368 Evaluate side-chains 143 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.5980 chunk 231 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 chunk 239 optimal weight: 10.0000 chunk 92 optimal weight: 0.0870 chunk 145 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 chunk 277 optimal weight: 7.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 188 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN B 188 ASN B 755 GLN B1002 GLN B1088 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24990 Z= 0.161 Angle : 0.557 12.754 34005 Z= 0.285 Chirality : 0.045 0.302 3960 Planarity : 0.004 0.068 4347 Dihedral : 6.342 59.149 3985 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.01 % Allowed : 12.04 % Favored : 85.94 % 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: 0.27 (0.15), residues: 3015 helix: 2.53 (0.21), residues: 645 sheet: 0.99 (0.20), residues: 657 loop : -1.16 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.003 0.001 HIS B1064 PHE 0.032 0.001 PHE C 133 TYR 0.016 0.001 TYR B1067 ARG 0.009 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 154 time to evaluate : 2.747 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.8647 (p) cc_final: 0.8294 (m) REVERT: A 237 ARG cc_start: 0.7924 (mtm180) cc_final: 0.7270 (mtm110) REVERT: A 309 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7815 (mp0) REVERT: B 121 ASN cc_start: 0.8319 (m-40) cc_final: 0.8013 (t0) REVERT: B 205 SER cc_start: 0.8744 (p) cc_final: 0.8324 (m) REVERT: B 237 ARG cc_start: 0.7926 (mtm180) cc_final: 0.7176 (mtm110) REVERT: B 309 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8084 (mp0) REVERT: B 357 ARG cc_start: 0.7409 (tpp-160) cc_final: 0.7206 (tpp80) REVERT: C 121 ASN cc_start: 0.8428 (m-40) cc_final: 0.8142 (t0) REVERT: C 160 TYR cc_start: 0.8129 (p90) cc_final: 0.7916 (p90) REVERT: C 210 ILE cc_start: 0.7988 (tp) cc_final: 0.7753 (pt) REVERT: C 220 PHE cc_start: 0.7437 (m-80) cc_final: 0.7076 (m-80) REVERT: C 237 ARG cc_start: 0.7899 (mtm180) cc_final: 0.6568 (mtm110) REVERT: C 309 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7690 (mp0) REVERT: C 357 ARG cc_start: 0.7404 (tpp-160) cc_final: 0.7107 (tpp80) REVERT: C 1045 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7989 (tttt) outliers start: 54 outliers final: 21 residues processed: 195 average time/residue: 1.0168 time to fit residues: 239.4547 Evaluate side-chains 152 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 278 optimal weight: 0.9980 chunk 300 optimal weight: 0.0770 chunk 247 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 223 optimal weight: 20.0000 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN B 394 ASN B 755 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24990 Z= 0.235 Angle : 0.555 10.549 34005 Z= 0.288 Chirality : 0.045 0.231 3960 Planarity : 0.004 0.049 4347 Dihedral : 5.943 56.743 3973 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.94 % Allowed : 12.83 % Favored : 85.23 % 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: 0.22 (0.15), residues: 3015 helix: 2.42 (0.21), residues: 648 sheet: 0.99 (0.20), residues: 657 loop : -1.18 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 886 HIS 0.006 0.001 HIS B1064 PHE 0.027 0.001 PHE C 133 TYR 0.018 0.001 TYR A1067 ARG 0.006 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 150 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8704 (p) cc_final: 0.8413 (m) REVERT: A 794 ILE cc_start: 0.8428 (tt) cc_final: 0.8213 (pp) REVERT: A 1002 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8449 (mp10) REVERT: B 121 ASN cc_start: 0.8207 (m-40) cc_final: 0.7810 (t0) REVERT: B 205 SER cc_start: 0.8725 (p) cc_final: 0.8416 (m) REVERT: B 237 ARG cc_start: 0.7947 (mtm180) cc_final: 0.6980 (mtm110) REVERT: B 309 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8153 (mp0) REVERT: C 121 ASN cc_start: 0.8435 (m-40) cc_final: 0.8037 (t0) REVERT: C 220 PHE cc_start: 0.7673 (m-80) cc_final: 0.7299 (m-80) REVERT: C 237 ARG cc_start: 0.7983 (mtm180) cc_final: 0.7021 (mtm110) REVERT: C 309 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7696 (mp0) outliers start: 52 outliers final: 27 residues processed: 193 average time/residue: 0.9100 time to fit residues: 216.4505 Evaluate side-chains 155 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 132 optimal weight: 0.0980 chunk 186 optimal weight: 3.9990 chunk 279 optimal weight: 0.9980 chunk 295 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 207 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B1002 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN C 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24990 Z= 0.276 Angle : 0.570 9.664 34005 Z= 0.299 Chirality : 0.046 0.226 3960 Planarity : 0.004 0.058 4347 Dihedral : 5.972 57.631 3973 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.27 % Allowed : 12.90 % Favored : 84.82 % 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: 0.16 (0.15), residues: 3015 helix: 2.36 (0.20), residues: 645 sheet: 0.71 (0.21), residues: 642 loop : -1.07 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.006 0.001 HIS B1064 PHE 0.022 0.001 PHE A 133 TYR 0.019 0.001 TYR A1067 ARG 0.009 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 140 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8763 (p) cc_final: 0.8453 (m) REVERT: A 309 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8065 (mp0) REVERT: A 558 LYS cc_start: 0.9097 (mmpt) cc_final: 0.8696 (mmpt) REVERT: A 794 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8273 (pp) REVERT: B 121 ASN cc_start: 0.8179 (m-40) cc_final: 0.7776 (t0) REVERT: B 205 SER cc_start: 0.8858 (p) cc_final: 0.8491 (m) REVERT: B 237 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7517 (mpp80) REVERT: B 309 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8214 (mp0) REVERT: C 176 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7972 (pt) REVERT: C 210 ILE cc_start: 0.7999 (tp) cc_final: 0.7707 (pp) REVERT: C 220 PHE cc_start: 0.7791 (m-80) cc_final: 0.7344 (m-80) REVERT: C 309 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7784 (mp0) REVERT: C 1045 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8430 (mmtt) outliers start: 61 outliers final: 28 residues processed: 194 average time/residue: 0.8929 time to fit residues: 214.0754 Evaluate side-chains 160 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 220 optimal weight: 0.0980 chunk 122 optimal weight: 0.7980 chunk 252 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 394 ASN B 755 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24990 Z= 0.174 Angle : 0.532 9.337 34005 Z= 0.276 Chirality : 0.045 0.241 3960 Planarity : 0.004 0.039 4347 Dihedral : 5.806 57.193 3973 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.24 % Allowed : 13.12 % Favored : 84.64 % 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: 0.22 (0.15), residues: 3015 helix: 2.41 (0.21), residues: 645 sheet: 0.97 (0.21), residues: 657 loop : -1.15 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 886 HIS 0.011 0.001 HIS A 207 PHE 0.031 0.001 PHE B 133 TYR 0.017 0.001 TYR B 160 ARG 0.004 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 138 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8689 (p) cc_final: 0.8441 (m) REVERT: A 309 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8069 (mp0) REVERT: A 558 LYS cc_start: 0.9094 (mmpt) cc_final: 0.8691 (mmpt) REVERT: A 794 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8296 (pp) REVERT: A 1045 LYS cc_start: 0.8524 (tttm) cc_final: 0.8145 (ttmm) REVERT: B 121 ASN cc_start: 0.8163 (m-40) cc_final: 0.7766 (t0) REVERT: B 205 SER cc_start: 0.8806 (p) cc_final: 0.8396 (m) REVERT: B 309 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8197 (mp0) REVERT: C 176 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7955 (pt) REVERT: C 220 PHE cc_start: 0.7763 (m-80) cc_final: 0.7345 (m-80) REVERT: C 309 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7707 (mp0) REVERT: C 558 LYS cc_start: 0.8957 (mmpt) cc_final: 0.8603 (mmpt) outliers start: 60 outliers final: 32 residues processed: 192 average time/residue: 0.8927 time to fit residues: 211.8542 Evaluate side-chains 161 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 3.9990 chunk 266 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 173 optimal weight: 3.9990 chunk 73 optimal weight: 0.0670 chunk 296 optimal weight: 0.0870 chunk 245 optimal weight: 0.5980 chunk 137 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 207 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24990 Z= 0.139 Angle : 0.517 8.734 34005 Z= 0.267 Chirality : 0.044 0.249 3960 Planarity : 0.004 0.054 4347 Dihedral : 5.648 56.594 3973 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.27 % Allowed : 12.98 % Favored : 84.75 % 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: 0.28 (0.15), residues: 3015 helix: 2.48 (0.21), residues: 645 sheet: 0.99 (0.21), residues: 657 loop : -1.11 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 886 HIS 0.018 0.001 HIS B 207 PHE 0.028 0.001 PHE C 338 TYR 0.018 0.001 TYR C 160 ARG 0.006 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 139 time to evaluate : 2.467 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.8728 (p) cc_final: 0.8447 (m) REVERT: A 237 ARG cc_start: 0.8051 (mtm180) cc_final: 0.7418 (mpp80) REVERT: A 309 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8000 (mp0) REVERT: A 558 LYS cc_start: 0.9093 (mmpt) cc_final: 0.8689 (mmpt) REVERT: A 794 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8272 (pp) REVERT: A 1045 LYS cc_start: 0.8457 (tttm) cc_final: 0.8090 (ttmm) REVERT: B 121 ASN cc_start: 0.8126 (m-40) cc_final: 0.7766 (t0) REVERT: B 205 SER cc_start: 0.8550 (p) cc_final: 0.8280 (m) REVERT: B 237 ARG cc_start: 0.8021 (mtm180) cc_final: 0.7545 (mpp80) REVERT: B 309 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8155 (mp0) REVERT: C 176 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7950 (pt) REVERT: C 210 ILE cc_start: 0.7867 (tp) cc_final: 0.7575 (pp) REVERT: C 220 PHE cc_start: 0.7731 (m-80) cc_final: 0.7312 (m-80) REVERT: C 309 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7675 (mp0) outliers start: 61 outliers final: 31 residues processed: 192 average time/residue: 0.8674 time to fit residues: 206.5465 Evaluate side-chains 158 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 125 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 168 optimal weight: 0.0170 chunk 216 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 249 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24990 Z= 0.179 Angle : 0.541 9.645 34005 Z= 0.277 Chirality : 0.045 0.240 3960 Planarity : 0.004 0.039 4347 Dihedral : 5.619 56.748 3973 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.01 % Allowed : 13.87 % Favored : 84.12 % 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: 0.27 (0.15), residues: 3015 helix: 2.48 (0.21), residues: 645 sheet: 1.02 (0.21), residues: 654 loop : -1.15 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 886 HIS 0.004 0.001 HIS B1064 PHE 0.029 0.001 PHE B 133 TYR 0.037 0.001 TYR A 380 ARG 0.006 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 137 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8747 (p) cc_final: 0.8465 (m) REVERT: A 309 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8045 (mp0) REVERT: A 558 LYS cc_start: 0.9094 (mmpt) cc_final: 0.8694 (mmpt) REVERT: A 780 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7919 (mt-10) REVERT: A 794 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8284 (pp) REVERT: A 1045 LYS cc_start: 0.8524 (tttm) cc_final: 0.8153 (ttmm) REVERT: B 121 ASN cc_start: 0.8178 (m-40) cc_final: 0.7745 (t0) REVERT: B 205 SER cc_start: 0.8567 (p) cc_final: 0.8301 (m) REVERT: B 237 ARG cc_start: 0.8075 (mtm180) cc_final: 0.7585 (mpp80) REVERT: B 309 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8178 (mp0) REVERT: C 176 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7943 (pt) REVERT: C 220 PHE cc_start: 0.7819 (m-80) cc_final: 0.7411 (m-80) REVERT: C 309 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7672 (mp0) REVERT: C 558 LYS cc_start: 0.8979 (mmpt) cc_final: 0.8644 (mmpt) outliers start: 54 outliers final: 33 residues processed: 181 average time/residue: 0.8282 time to fit residues: 188.7012 Evaluate side-chains 159 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 231 optimal weight: 0.3980 chunk 268 optimal weight: 4.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24990 Z= 0.261 Angle : 0.576 8.174 34005 Z= 0.300 Chirality : 0.046 0.241 3960 Planarity : 0.004 0.050 4347 Dihedral : 5.787 57.957 3973 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.98 % Allowed : 13.87 % Favored : 84.15 % 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: 0.14 (0.15), residues: 3015 helix: 2.34 (0.20), residues: 645 sheet: 0.77 (0.21), residues: 624 loop : -1.10 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 886 HIS 0.010 0.001 HIS B 207 PHE 0.026 0.002 PHE A 133 TYR 0.023 0.001 TYR A 904 ARG 0.005 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 136 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8780 (p) cc_final: 0.8487 (m) REVERT: A 309 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8196 (mp0) REVERT: A 558 LYS cc_start: 0.9086 (mmpt) cc_final: 0.8658 (mmpt) REVERT: A 794 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8339 (pp) REVERT: A 1045 LYS cc_start: 0.8576 (tttm) cc_final: 0.8188 (ttmm) REVERT: B 205 SER cc_start: 0.8671 (p) cc_final: 0.8453 (m) REVERT: B 237 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7647 (mpp80) REVERT: B 309 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8212 (mp0) REVERT: C 176 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7965 (pt) REVERT: C 309 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7762 (mp0) REVERT: C 558 LYS cc_start: 0.8947 (mmpt) cc_final: 0.8621 (mmpt) outliers start: 53 outliers final: 31 residues processed: 180 average time/residue: 0.9187 time to fit residues: 203.9013 Evaluate side-chains 157 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 259 optimal weight: 6.9990 chunk 273 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 24990 Z= 0.293 Angle : 0.588 8.715 34005 Z= 0.306 Chirality : 0.046 0.245 3960 Planarity : 0.004 0.050 4347 Dihedral : 5.874 58.837 3972 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.60 % Allowed : 14.39 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3015 helix: 2.23 (0.20), residues: 645 sheet: 0.72 (0.21), residues: 624 loop : -1.13 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 886 HIS 0.011 0.001 HIS B 207 PHE 0.027 0.002 PHE C 565 TYR 0.024 0.002 TYR A 904 ARG 0.005 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 130 time to evaluate : 2.569 Fit side-chains REVERT: A 100 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8761 (mm) REVERT: A 205 SER cc_start: 0.8758 (p) cc_final: 0.8462 (m) REVERT: A 237 ARG cc_start: 0.8103 (mtm180) cc_final: 0.7372 (mtm110) REVERT: A 309 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8205 (mp0) REVERT: A 380 TYR cc_start: 0.7654 (m-10) cc_final: 0.7274 (m-10) REVERT: A 558 LYS cc_start: 0.9078 (mmpt) cc_final: 0.8653 (mmpt) REVERT: A 794 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8418 (pp) REVERT: B 205 SER cc_start: 0.8729 (p) cc_final: 0.8458 (m) REVERT: B 237 ARG cc_start: 0.8150 (mtm180) cc_final: 0.7122 (mtm-85) REVERT: B 309 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8267 (mp0) REVERT: C 176 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7987 (pt) REVERT: C 237 ARG cc_start: 0.8122 (mtm180) cc_final: 0.7055 (mtm110) REVERT: C 309 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7722 (mp0) REVERT: C 558 LYS cc_start: 0.9000 (mmpt) cc_final: 0.8654 (mmpt) outliers start: 43 outliers final: 32 residues processed: 166 average time/residue: 0.8644 time to fit residues: 179.6704 Evaluate side-chains 154 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 119 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 202 optimal weight: 0.4980 chunk 304 optimal weight: 3.9990 chunk 280 optimal weight: 0.8980 chunk 242 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 187 optimal weight: 0.0170 chunk 148 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24990 Z= 0.168 Angle : 0.549 8.900 34005 Z= 0.284 Chirality : 0.045 0.262 3960 Planarity : 0.004 0.038 4347 Dihedral : 5.672 57.662 3972 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.53 % Allowed : 14.73 % Favored : 83.74 % 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: 0.20 (0.15), residues: 3015 helix: 2.39 (0.21), residues: 645 sheet: 0.80 (0.21), residues: 624 loop : -1.06 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.011 0.001 HIS B 207 PHE 0.026 0.001 PHE A 133 TYR 0.019 0.001 TYR A 160 ARG 0.006 0.000 ARG C 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 131 time to evaluate : 2.562 Fit side-chains revert: symmetry clash REVERT: A 100 ILE cc_start: 0.9028 (mm) cc_final: 0.8822 (mp) REVERT: A 205 SER cc_start: 0.8723 (p) cc_final: 0.8410 (m) REVERT: A 237 ARG cc_start: 0.8125 (mtm180) cc_final: 0.7370 (mtm110) REVERT: A 309 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8164 (mp0) REVERT: A 558 LYS cc_start: 0.9079 (mmpt) cc_final: 0.8650 (mmpt) REVERT: A 794 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8406 (pp) REVERT: B 205 SER cc_start: 0.8765 (p) cc_final: 0.8460 (m) REVERT: B 237 ARG cc_start: 0.8158 (mtm180) cc_final: 0.7070 (mtm-85) REVERT: B 309 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8207 (mp0) REVERT: C 176 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7959 (pt) REVERT: C 309 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7697 (mp0) REVERT: C 558 LYS cc_start: 0.8999 (mmpt) cc_final: 0.8649 (mmpt) outliers start: 41 outliers final: 32 residues processed: 165 average time/residue: 0.8467 time to fit residues: 174.7817 Evaluate side-chains 158 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 223 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 249 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 213 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 370 ASN B 394 ASN C 370 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.131361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.075937 restraints weight = 45820.492| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.82 r_work: 0.2915 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24990 Z= 0.168 Angle : 0.548 8.191 34005 Z= 0.283 Chirality : 0.045 0.251 3960 Planarity : 0.004 0.037 4347 Dihedral : 5.614 57.390 3972 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.53 % Allowed : 15.03 % Favored : 83.45 % 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: 0.14 (0.15), residues: 3015 helix: 2.22 (0.21), residues: 663 sheet: 0.82 (0.21), residues: 624 loop : -1.10 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.014 0.001 HIS C 505 PHE 0.020 0.001 PHE C 133 TYR 0.029 0.001 TYR C 453 ARG 0.005 0.000 ARG C 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6696.17 seconds wall clock time: 119 minutes 53.64 seconds (7193.64 seconds total)