Starting phenix.real_space_refine on Tue Oct 15 06:55:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0g_28756/10_2024/8f0g_28756.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0g_28756/10_2024/8f0g_28756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0g_28756/10_2024/8f0g_28756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0g_28756/10_2024/8f0g_28756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0g_28756/10_2024/8f0g_28756.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0g_28756/10_2024/8f0g_28756.cif" } resolution = 3.35 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= 0.020 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 96 5.16 5 C 12483 2.51 5 N 3246 2.21 5 O 3810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 19635 Number of models: 1 Model: "" Number of chains: 11 Chain: "X" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 888 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain breaks: 1 Chain: "Y" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 744 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 91} Chain breaks: 1 Chain: "A" Number of atoms: 6684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 860, 6684 Classifications: {'peptide': 860} Link IDs: {'PTRANS': 45, 'TRANS': 814} Chain breaks: 12 Chain: "B" Number of atoms: 4740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4740 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 32, 'TRANS': 584} Chain breaks: 4 Chain: "C" Number of atoms: 6243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6243 Classifications: {'peptide': 803} Link IDs: {'PTRANS': 42, 'TRANS': 760} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 12.37, per 1000 atoms: 0.63 Number of scatterers: 19635 At special positions: 0 Unit cell: (108.24, 118.8, 194.04, 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 96 16.00 O 3810 8.00 N 3246 7.00 C 12483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 24 " - pdb=" SG CYS Y 89 " distance=2.03 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 391 " - pdb=" SG CYS A 525 " distance=2.02 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=2.04 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 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG B1301 " - " ASN B 801 " " NAG B1302 " - " ASN B 717 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B1134 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C 717 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN C 801 " Time building additional restraints: 5.13 Conformation dependent library (CDL) restraints added in 2.6 seconds 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4666 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 41 sheets defined 28.1% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'X' and resid 101 through 105 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.616A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 630 through 636 removed outlier: 3.900A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.758A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.612A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.538A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 removed outlier: 3.624A pdb=" N PHE A 855 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 906 Processing helix chain 'A' and resid 907 through 910 removed outlier: 3.520A pdb=" N GLY A 910 " --> pdb=" O ASN A 907 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.329A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.555A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.906A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 984 removed outlier: 3.615A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.755A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 4.275A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.872A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.816A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.528A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.708A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.585A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 957 " --> pdb=" O ASN B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.531A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.608A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.470A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.777A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.644A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 827 removed outlier: 3.830A pdb=" N THR C 827 " --> pdb=" O PHE C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 856 removed outlier: 4.062A pdb=" N LYS C 854 " --> pdb=" O CYS C 851 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 855 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.179A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.823A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.304A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.522A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.936A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.622A 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 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.675A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'X' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'X' and resid 59 through 60 removed outlier: 6.684A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN X 39 " --> pdb=" O LEU X 93 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU X 93 " --> pdb=" O GLN X 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 5 through 7 removed outlier: 3.755A pdb=" N THR Y 6 " --> pdb=" O ARG Y 25 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG Y 25 " --> pdb=" O THR Y 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'Y' and resid 20 through 22 Processing sheet with id=AA5, first strand: chain 'Y' and resid 45 through 49 removed outlier: 6.565A pdb=" N TRP Y 36 " --> pdb=" O LEU Y 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.058A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.897A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.498A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 316 removed outlier: 3.969A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.932A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.564A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.523A pdb=" N PHE A 392 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.721A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.839A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 725 through 727 removed outlier: 4.616A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.543A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.668A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1086 through 1087 Processing sheet with id=AC1, first strand: chain 'B' and resid 275 through 279 removed outlier: 4.546A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.532A pdb=" N ILE B 598 " --> pdb=" O ALA B 609 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.750A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.582A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AC7, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.486A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.486A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.716A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 278 through 279 removed outlier: 4.085A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.329A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.219A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.620A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.219A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.620A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.712A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.647A pdb=" N ARG C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD9, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.593A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 660 removed outlier: 3.622A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.573A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 717 through 728 removed outlier: 5.977A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.484A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.970A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) 759 hydrogen bonds defined for protein. 2091 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: 8.51 Time building geometry restraints manager: 5.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6067 1.33 - 1.45: 3662 1.45 - 1.58: 10196 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 20048 Sorted by residual: bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.65e+00 bond pdb=" CA SER C 884 " pdb=" CB SER C 884 " ideal model delta sigma weight residual 1.534 1.484 0.050 2.33e-02 1.84e+03 4.60e+00 bond pdb=" CB ASN A 914 " pdb=" CG ASN A 914 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.94e+00 bond pdb=" CB ASN B 914 " pdb=" CG ASN B 914 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.63e+00 ... (remaining 20043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 26837 1.99 - 3.98: 373 3.98 - 5.97: 38 5.97 - 7.95: 13 7.95 - 9.94: 3 Bond angle restraints: 27264 Sorted by residual: angle pdb=" CA ILE B 285 " pdb=" CB ILE B 285 " pdb=" CG1 ILE B 285 " ideal model delta sigma weight residual 110.40 116.18 -5.78 1.70e+00 3.46e-01 1.16e+01 angle pdb=" N ASN A 234 " pdb=" CA ASN A 234 " pdb=" CB ASN A 234 " ideal model delta sigma weight residual 109.48 114.67 -5.19 1.55e+00 4.16e-01 1.12e+01 angle pdb=" C2 NAG A1307 " pdb=" N2 NAG A1307 " pdb=" C7 NAG A1307 " ideal model delta sigma weight residual 124.56 134.50 -9.94 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CB ILE B 285 " pdb=" CG1 ILE B 285 " pdb=" CD1 ILE B 285 " ideal model delta sigma weight residual 113.80 120.66 -6.86 2.10e+00 2.27e-01 1.07e+01 angle pdb=" C ASN A 61 " pdb=" CA ASN A 61 " pdb=" CB ASN A 61 " ideal model delta sigma weight residual 109.70 115.14 -5.44 1.81e+00 3.05e-01 9.03e+00 ... (remaining 27259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 11364 21.30 - 42.60: 805 42.60 - 63.90: 145 63.90 - 85.20: 22 85.20 - 106.50: 7 Dihedral angle restraints: 12343 sinusoidal: 5112 harmonic: 7231 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 150.07 -57.07 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -138.01 52.01 1 1.00e+01 1.00e-02 3.69e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -135.05 49.05 1 1.00e+01 1.00e-02 3.31e+01 ... (remaining 12340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 3112 0.118 - 0.235: 92 0.235 - 0.353: 6 0.353 - 0.470: 1 0.470 - 0.588: 1 Chirality restraints: 3212 Sorted by residual: chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.65e+00 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 717 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 3209 not shown) Planarity restraints: 3502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " -0.175 2.00e-02 2.50e+03 1.71e-01 3.67e+02 pdb=" C7 NAG A1307 " -0.090 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.018 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " 0.320 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1308 " -0.100 2.00e-02 2.50e+03 8.81e-02 9.70e+01 pdb=" C7 NAG A1308 " -0.024 2.00e-02 2.50e+03 pdb=" C8 NAG A1308 " -0.059 2.00e-02 2.50e+03 pdb=" N2 NAG A1308 " 0.155 2.00e-02 2.50e+03 pdb=" O7 NAG A1308 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.004 2.00e-02 2.50e+03 3.92e-02 1.92e+01 pdb=" CG ASN A 61 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " 0.048 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.034 2.00e-02 2.50e+03 ... (remaining 3499 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4229 2.77 - 3.30: 18874 3.30 - 3.84: 32182 3.84 - 4.37: 36827 4.37 - 4.90: 63885 Nonbonded interactions: 155997 Sorted by model distance: nonbonded pdb=" O SER B 708 " pdb=" OG SER B 711 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR A1076 " pdb=" OG SER A1097 " model vdw 2.245 3.040 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.276 3.040 nonbonded pdb=" OG SER A 383 " pdb=" OD1 ASP B 985 " model vdw 2.298 3.040 ... (remaining 155992 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 'D' selection = chain 'E' selection = chain 'F' } 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: 9.400 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 47.460 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.090 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.011 0.069 20048 Z= 0.719 Angle : 0.634 9.942 27264 Z= 0.347 Chirality : 0.058 0.588 3212 Planarity : 0.005 0.171 3481 Dihedral : 14.455 106.499 7584 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.14 % Allowed : 16.61 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % 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 (0.17), residues: 2438 helix: 1.61 (0.21), residues: 612 sheet: -0.44 (0.24), residues: 478 loop : -0.83 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 886 HIS 0.008 0.002 HIS C1058 PHE 0.021 0.003 PHE A 86 TYR 0.025 0.002 TYR A 904 ARG 0.013 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 30 ASP cc_start: 0.8511 (m-30) cc_final: 0.8193 (t0) REVERT: X 60 TYR cc_start: 0.7931 (m-80) cc_final: 0.7489 (m-80) REVERT: X 84 ASN cc_start: 0.8485 (p0) cc_final: 0.8106 (m110) REVERT: Y 40 LYS cc_start: 0.8633 (mptm) cc_final: 0.8172 (mmmt) REVERT: Y 48 LEU cc_start: 0.8804 (mt) cc_final: 0.8538 (mp) REVERT: Y 56 GLU cc_start: 0.8410 (tp30) cc_final: 0.7102 (mp0) REVERT: Y 97 LEU cc_start: 0.8480 (mm) cc_final: 0.8262 (mm) outliers start: 3 outliers final: 2 residues processed: 102 average time/residue: 0.3521 time to fit residues: 55.8058 Evaluate side-chains 84 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain C residue 488 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 117 optimal weight: 0.2980 chunk 144 optimal weight: 0.6980 chunk 224 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 955 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN C 641 ASN C 751 ASN C1011 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20048 Z= 0.184 Angle : 0.541 11.656 27264 Z= 0.277 Chirality : 0.044 0.375 3212 Planarity : 0.004 0.051 3481 Dihedral : 7.016 65.554 3152 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.80 % Allowed : 15.04 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2438 helix: 2.04 (0.21), residues: 615 sheet: -0.24 (0.23), residues: 475 loop : -0.83 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS A1083 PHE 0.014 0.001 PHE B 759 TYR 0.023 0.001 TYR B1067 ARG 0.013 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 93 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 30 ASP cc_start: 0.8407 (m-30) cc_final: 0.8138 (t0) REVERT: X 31 ASP cc_start: 0.8548 (m-30) cc_final: 0.8187 (m-30) REVERT: X 60 TYR cc_start: 0.7906 (m-80) cc_final: 0.7493 (m-80) REVERT: X 116 TRP cc_start: 0.8158 (m100) cc_final: 0.7713 (m100) REVERT: Y 56 GLU cc_start: 0.8410 (tp30) cc_final: 0.7415 (mp0) REVERT: A 906 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8056 (m-10) REVERT: C 375 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7308 (m-10) REVERT: C 984 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.7888 (tp) outliers start: 39 outliers final: 13 residues processed: 125 average time/residue: 0.3206 time to fit residues: 64.2352 Evaluate side-chains 97 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: