Starting phenix.real_space_refine on Sat May 24 04:18:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ukf_42353/05_2025/8ukf_42353.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ukf_42353/05_2025/8ukf_42353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ukf_42353/05_2025/8ukf_42353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ukf_42353/05_2025/8ukf_42353.map" model { file = "/net/cci-nas-00/data/ceres_data/8ukf_42353/05_2025/8ukf_42353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ukf_42353/05_2025/8ukf_42353.cif" } resolution = 3.1 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= 0.064 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 114 5.16 5 C 15925 2.51 5 N 4103 2.21 5 O 4822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24964 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "B" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "C" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 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: "G" 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: "H" 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: "I" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 14.64, per 1000 atoms: 0.59 Number of scatterers: 24964 At special positions: 0 Unit cell: (136.08, 133.92, 173.88, 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 114 16.00 O 4822 8.00 N 4103 7.00 C 15925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 801 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 801 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 234 " " NAG C1310 " - " ASN C 801 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN C 717 " " NAG I 1 " - " ASN C1098 " Time building additional restraints: 6.18 Conformation dependent library (CDL) restraints added in 3.2 seconds 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5862 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 48 sheets defined 26.0% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.837A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.699A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.987A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.628A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.554A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 842 removed outlier: 3.512A pdb=" N GLY A 842 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.570A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.601A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.537A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.657A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.774A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.521A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.962A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 368 removed outlier: 4.015A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.800A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.763A 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 836 through 842 removed outlier: 3.527A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.543A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.603A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.675A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.747A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (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 984 Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.923A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.814A pdb=" N ASN C 343 " --> pdb=" O HIS C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.881A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.811A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.722A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.558A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.644A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 842 Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.523A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.542A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.559A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.696A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.688A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (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 Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.924A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.842A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.857A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.950A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.508A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'A' and resid 140 through 142 removed outlier: 5.297A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.178A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.609A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.279A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.080A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.618A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.986A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.573A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.770A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.544A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.420A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.009A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.157A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.130A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.681A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.553A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.981A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.568A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.948A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.612A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 25 through 30 removed outlier: 3.795A pdb=" N THR C 25 " --> pdb=" O HIS C 66 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.383A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.610A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.206A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 324 through 325 removed outlier: 7.115A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.668A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.628A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.990A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.577A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.182A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.549A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 961 hydrogen bonds defined for protein. 2658 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.74 Time building geometry restraints manager: 7.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7941 1.35 - 1.47: 6505 1.47 - 1.60: 10935 1.60 - 1.72: 0 1.72 - 1.85: 141 Bond restraints: 25522 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.37e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.28e+00 bond pdb=" C LYS A 811 " pdb=" N PRO A 812 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.30e-02 5.92e+03 5.22e+00 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.01e+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 4.65e+00 ... (remaining 25517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 34426 3.23 - 6.46: 256 6.46 - 9.69: 36 9.69 - 12.92: 1 12.92 - 16.14: 2 Bond angle restraints: 34721 Sorted by residual: angle pdb=" CA CYS C 525 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 114.40 130.54 -16.14 2.30e+00 1.89e-01 4.93e+01 angle pdb=" CA VAL C 620 " pdb=" C VAL C 620 " pdb=" N PRO C 621 " ideal model delta sigma weight residual 120.83 124.39 -3.56 6.10e-01 2.69e+00 3.40e+01 angle pdb=" CA CYS C 391 " pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " ideal model delta sigma weight residual 114.40 127.32 -12.92 2.30e+00 1.89e-01 3.16e+01 angle pdb=" C GLU C 619 " pdb=" N VAL C 620 " pdb=" CA VAL C 620 " ideal model delta sigma weight residual 120.33 124.76 -4.43 8.00e-01 1.56e+00 3.06e+01 angle pdb=" N VAL C 620 " pdb=" CA VAL C 620 " pdb=" C VAL C 620 " ideal model delta sigma weight residual 112.35 118.31 -5.96 1.20e+00 6.94e-01 2.46e+01 ... (remaining 34716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14194 17.95 - 35.91: 1281 35.91 - 53.86: 211 53.86 - 71.82: 51 71.82 - 89.77: 43 Dihedral angle restraints: 15780 sinusoidal: 6675 harmonic: 9105 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 -177.62 -89.38 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual -86.00 -12.58 -73.42 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 158.17 -65.17 1 1.00e+01 1.00e-02 5.57e+01 ... (remaining 15777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3578 0.087 - 0.174: 460 0.174 - 0.261: 26 0.261 - 0.348: 4 0.348 - 0.435: 1 Chirality restraints: 4069 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CG LEU C 390 " pdb=" CB LEU C 390 " pdb=" CD1 LEU C 390 " pdb=" CD2 LEU C 390 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 4066 not shown) Planarity restraints: 4471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO C 521 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.033 2.00e-02 2.50e+03 3.08e-02 1.18e+01 pdb=" CG ASN A 709 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.033 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 886 " -0.023 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP B 886 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP B 886 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 886 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 886 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 886 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 886 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 886 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 886 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 886 " -0.003 2.00e-02 2.50e+03 ... (remaining 4468 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6359 2.80 - 3.33: 19655 3.33 - 3.85: 39963 3.85 - 4.38: 45106 4.38 - 4.90: 81850 Nonbonded interactions: 192933 Sorted by model distance: nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.279 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.294 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR A 599 " pdb=" O PRO A 600 " model vdw 2.320 3.040 nonbonded pdb=" OE2 GLU A 516 " pdb=" OH TYR C 200 " model vdw 2.320 3.040 ... (remaining 192928 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' and (resid 24 through 1147 or resid 1301 through 1309)) selection = (chain 'C' and (resid 24 through 1147 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 2.310 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: 0.930 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 56.690 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 : 0.006 0.088 25605 Z= 0.257 Angle : 0.827 16.144 34928 Z= 0.430 Chirality : 0.056 0.435 4069 Planarity : 0.006 0.089 4436 Dihedral : 14.342 89.770 9792 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 3081 helix: -0.43 (0.17), residues: 707 sheet: 0.17 (0.20), residues: 650 loop : -1.51 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP B 886 HIS 0.007 0.001 HIS B1048 PHE 0.048 0.003 PHE B 906 TYR 0.021 0.002 TYR B 28 ARG 0.013 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00537 ( 35) link_NAG-ASN : angle 2.37302 ( 105) link_BETA1-4 : bond 0.00754 ( 6) link_BETA1-4 : angle 1.99976 ( 18) hydrogen bonds : bond 0.20025 ( 959) hydrogen bonds : angle 7.48454 ( 2658) SS BOND : bond 0.00716 ( 42) SS BOND : angle 2.59186 ( 84) covalent geometry : bond 0.00590 (25522) covalent geometry : angle 0.80736 (34721) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 207 HIS cc_start: 0.7581 (t70) cc_final: 0.6889 (t-90) REVERT: C 467 ASP cc_start: 0.7184 (t0) cc_final: 0.6911 (t70) REVERT: C 950 ASP cc_start: 0.7935 (m-30) cc_final: 0.7698 (m-30) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.3670 time to fit residues: 121.6602 Evaluate side-chains 172 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 182 optimal weight: 0.4980 chunk 283 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 448 ASN B 901 GLN C 271 GLN C 360 ASN C 914 ASN C 935 GLN C1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.177509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.109415 restraints weight = 26475.243| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.38 r_work: 0.2920 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25605 Z= 0.118 Angle : 0.535 7.407 34928 Z= 0.278 Chirality : 0.044 0.293 4069 Planarity : 0.004 0.062 4436 Dihedral : 5.948 52.031 4203 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.52 % Allowed : 5.23 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.45 (0.14), residues: 3081 helix: 1.14 (0.19), residues: 713 sheet: 0.49 (0.20), residues: 681 loop : -1.33 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 886 HIS 0.003 0.001 HIS C 339 PHE 0.021 0.001 PHE A 168 TYR 0.014 0.001 TYR C 265 ARG 0.004 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 35) link_NAG-ASN : angle 1.71256 ( 105) link_BETA1-4 : bond 0.00322 ( 6) link_BETA1-4 : angle 1.17981 ( 18) hydrogen bonds : bond 0.05139 ( 959) hydrogen bonds : angle 5.40201 ( 2658) SS BOND : bond 0.00278 ( 42) SS BOND : angle 1.59193 ( 84) covalent geometry : bond 0.00269 (25522) covalent geometry : angle 0.52134 (34721) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 2.746 Fit side-chains revert: symmetry clash REVERT: A 361 CYS cc_start: 0.7646 (p) cc_final: 0.7303 (p) REVERT: B 237 ARG cc_start: 0.7137 (mtp85) cc_final: 0.6865 (mtp85) REVERT: C 453 TYR cc_start: 0.6404 (p90) cc_final: 0.6161 (p90) REVERT: C 467 ASP cc_start: 0.7115 (t0) cc_final: 0.6832 (t70) REVERT: C 902 MET cc_start: 0.9036 (mmm) cc_final: 0.8737 (mmt) REVERT: C 935 GLN cc_start: 0.7128 (tm130) cc_final: 0.6567 (tm-30) REVERT: C 950 ASP cc_start: 0.8447 (m-30) cc_final: 0.8210 (m-30) outliers start: 14 outliers final: 10 residues processed: 214 average time/residue: 0.3637 time to fit residues: 123.9717 Evaluate side-chains 191 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 169 optimal weight: 0.5980 chunk 138 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 116 optimal weight: 0.0040 chunk 122 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 overall best weight: 1.0594 ------------------------------------------------------------------------------- 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN C 207 HIS C 271 GLN C 824 ASN C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.177077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.109570 restraints weight = 26416.357| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.37 r_work: 0.2906 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25605 Z= 0.129 Angle : 0.517 7.817 34928 Z= 0.267 Chirality : 0.044 0.265 4069 Planarity : 0.004 0.055 4436 Dihedral : 5.477 51.601 4203 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.96 % Allowed : 6.96 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.25 (0.15), residues: 3081 helix: 1.43 (0.20), residues: 735 sheet: 0.54 (0.19), residues: 672 loop : -1.24 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.003 0.001 HIS C 339 PHE 0.022 0.001 PHE A 168 TYR 0.020 0.001 TYR B 170 ARG 0.005 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 35) link_NAG-ASN : angle 1.61675 ( 105) link_BETA1-4 : bond 0.00381 ( 6) link_BETA1-4 : angle 1.16442 ( 18) hydrogen bonds : bond 0.05055 ( 959) hydrogen bonds : angle 5.02849 ( 2658) SS BOND : bond 0.00282 ( 42) SS BOND : angle 1.44423 ( 84) covalent geometry : bond 0.00310 (25522) covalent geometry : angle 0.50473 (34721) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 2.541 Fit side-chains revert: symmetry clash REVERT: A 361 CYS cc_start: 0.7731 (p) cc_final: 0.7347 (p) REVERT: B 191 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8146 (mt-10) REVERT: C 189 LEU cc_start: 0.6388 (mp) cc_final: 0.6120 (mp) REVERT: C 453 TYR cc_start: 0.6626 (p90) cc_final: 0.6393 (p90) REVERT: C 467 ASP cc_start: 0.7272 (t0) cc_final: 0.6953 (t70) REVERT: C 902 MET cc_start: 0.9026 (mmm) cc_final: 0.8728 (mmt) REVERT: C 935 GLN cc_start: 0.7159 (tm130) cc_final: 0.6586 (tm-30) REVERT: C 950 ASP cc_start: 0.8417 (m-30) cc_final: 0.8183 (m-30) REVERT: C 1138 TYR cc_start: 0.7903 (t80) cc_final: 0.7399 (t80) outliers start: 26 outliers final: 17 residues processed: 216 average time/residue: 0.3555 time to fit residues: 122.1646 Evaluate side-chains 205 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 245 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 179 optimal weight: 0.2980 chunk 253 optimal weight: 0.7980 chunk 77 optimal weight: 0.0270 chunk 240 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 218 optimal weight: 0.0030 chunk 97 optimal weight: 0.7980 overall best weight: 0.3848 ------------------------------------------------------------------------------- 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 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 519 HIS C 207 HIS C 271 GLN C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.178880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.111556 restraints weight = 26769.904| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.38 r_work: 0.2944 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25605 Z= 0.087 Angle : 0.461 7.336 34928 Z= 0.240 Chirality : 0.042 0.233 4069 Planarity : 0.003 0.050 4436 Dihedral : 5.012 53.229 4203 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.14 % Allowed : 8.10 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3081 helix: 1.79 (0.20), residues: 737 sheet: 0.64 (0.20), residues: 676 loop : -1.09 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.004 0.000 HIS A 519 PHE 0.023 0.001 PHE A 168 TYR 0.013 0.001 TYR B1067 ARG 0.005 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 35) link_NAG-ASN : angle 1.41927 ( 105) link_BETA1-4 : bond 0.00363 ( 6) link_BETA1-4 : angle 1.04924 ( 18) hydrogen bonds : bond 0.04001 ( 959) hydrogen bonds : angle 4.66535 ( 2658) SS BOND : bond 0.00244 ( 42) SS BOND : angle 1.33262 ( 84) covalent geometry : bond 0.00189 (25522) covalent geometry : angle 0.45078 (34721) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 2.715 Fit side-chains revert: symmetry clash REVERT: A 105 ILE cc_start: 0.7215 (pt) cc_final: 0.6931 (mt) REVERT: A 117 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5733 (tt) REVERT: A 361 CYS cc_start: 0.7612 (p) cc_final: 0.7235 (p) REVERT: A 516 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7150 (mt-10) REVERT: B 191 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8128 (mt-10) REVERT: B 237 ARG cc_start: 0.7220 (mtp85) cc_final: 0.7002 (mtp85) REVERT: B 332 ILE cc_start: 0.7951 (pt) cc_final: 0.7676 (mt) REVERT: B 420 ASP cc_start: 0.7985 (m-30) cc_final: 0.7619 (m-30) REVERT: B 955 ASN cc_start: 0.8088 (m-40) cc_final: 0.7775 (m110) REVERT: C 287 ASP cc_start: 0.8545 (t0) cc_final: 0.8176 (t0) REVERT: C 291 CYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7178 (m) REVERT: C 467 ASP cc_start: 0.7258 (t0) cc_final: 0.6914 (t70) REVERT: C 902 MET cc_start: 0.9032 (mmm) cc_final: 0.8642 (mmt) REVERT: C 935 GLN cc_start: 0.7078 (tm130) cc_final: 0.6494 (tm-30) REVERT: C 950 ASP cc_start: 0.8322 (m-30) cc_final: 0.8084 (m-30) REVERT: C 1138 TYR cc_start: 0.7865 (t80) cc_final: 0.7350 (t80) outliers start: 31 outliers final: 17 residues processed: 224 average time/residue: 0.3440 time to fit residues: 125.2646 Evaluate side-chains 206 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 200 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 299 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 519 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 271 GLN C1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.174182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.110833 restraints weight = 26477.127| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.67 r_work: 0.2825 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25605 Z= 0.207 Angle : 0.592 8.010 34928 Z= 0.303 Chirality : 0.047 0.281 4069 Planarity : 0.004 0.050 4436 Dihedral : 5.446 53.458 4203 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.55 % Allowed : 8.91 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.21 (0.15), residues: 3081 helix: 1.64 (0.20), residues: 721 sheet: 0.39 (0.19), residues: 664 loop : -1.19 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 886 HIS 0.006 0.001 HIS A 519 PHE 0.025 0.002 PHE A 377 TYR 0.017 0.002 TYR A 837 ARG 0.006 0.001 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 35) link_NAG-ASN : angle 1.77274 ( 105) link_BETA1-4 : bond 0.00321 ( 6) link_BETA1-4 : angle 1.22880 ( 18) hydrogen bonds : bond 0.06012 ( 959) hydrogen bonds : angle 4.96352 ( 2658) SS BOND : bond 0.00385 ( 42) SS BOND : angle 1.82008 ( 84) covalent geometry : bond 0.00516 (25522) covalent geometry : angle 0.57768 (34721) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 2.655 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5901 (tt) REVERT: A 237 ARG cc_start: 0.7339 (mmt90) cc_final: 0.6717 (mpt-90) REVERT: A 347 PHE cc_start: 0.8839 (m-10) cc_final: 0.8575 (m-10) REVERT: A 361 CYS cc_start: 0.7718 (p) cc_final: 0.7287 (p) REVERT: B 237 ARG cc_start: 0.7339 (mtp85) cc_final: 0.7113 (mtp85) REVERT: B 332 ILE cc_start: 0.8080 (pt) cc_final: 0.7701 (mt) REVERT: B 420 ASP cc_start: 0.8166 (m-30) cc_final: 0.7727 (m-30) REVERT: B 462 LYS cc_start: 0.6987 (mptt) cc_final: 0.6361 (mttm) REVERT: C 189 LEU cc_start: 0.6403 (mp) cc_final: 0.6158 (mp) REVERT: C 287 ASP cc_start: 0.8647 (t0) cc_final: 0.8263 (t0) REVERT: C 291 CYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7304 (m) REVERT: C 462 LYS cc_start: 0.7239 (mtpt) cc_final: 0.6470 (mptt) REVERT: C 467 ASP cc_start: 0.7407 (t0) cc_final: 0.7032 (t70) REVERT: C 537 LYS cc_start: 0.7383 (mtmm) cc_final: 0.6820 (mtpp) REVERT: C 902 MET cc_start: 0.9019 (mmm) cc_final: 0.8784 (mmt) REVERT: C 935 GLN cc_start: 0.7337 (tm130) cc_final: 0.6759 (tm-30) REVERT: C 950 ASP cc_start: 0.8466 (m-30) cc_final: 0.8250 (m-30) REVERT: C 1138 TYR cc_start: 0.7914 (t80) cc_final: 0.7482 (t80) outliers start: 42 outliers final: 31 residues processed: 238 average time/residue: 0.3635 time to fit residues: 138.2126 Evaluate side-chains 229 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 185 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 310 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 chunk 287 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 935 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 271 GLN C 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.172713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.107076 restraints weight = 26493.659| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.55 r_work: 0.2839 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25605 Z= 0.145 Angle : 0.528 8.111 34928 Z= 0.273 Chirality : 0.044 0.261 4069 Planarity : 0.003 0.048 4436 Dihedral : 5.340 59.237 4203 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.92 % Allowed : 9.76 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3081 helix: 1.78 (0.20), residues: 719 sheet: 0.46 (0.19), residues: 674 loop : -1.17 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 64 HIS 0.007 0.001 HIS A 519 PHE 0.018 0.001 PHE A 168 TYR 0.014 0.001 TYR B1067 ARG 0.005 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 35) link_NAG-ASN : angle 1.64256 ( 105) link_BETA1-4 : bond 0.00347 ( 6) link_BETA1-4 : angle 1.15627 ( 18) hydrogen bonds : bond 0.05183 ( 959) hydrogen bonds : angle 4.80353 ( 2658) SS BOND : bond 0.00328 ( 42) SS BOND : angle 1.62631 ( 84) covalent geometry : bond 0.00353 (25522) covalent geometry : angle 0.51502 (34721) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 2.495 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5917 (tt) REVERT: A 237 ARG cc_start: 0.7165 (mmt90) cc_final: 0.6493 (mpt-90) REVERT: A 361 CYS cc_start: 0.7555 (p) cc_final: 0.7078 (p) REVERT: B 237 ARG cc_start: 0.7251 (mtp85) cc_final: 0.7008 (mtp85) REVERT: B 332 ILE cc_start: 0.8009 (pt) cc_final: 0.7666 (mt) REVERT: B 420 ASP cc_start: 0.8174 (m-30) cc_final: 0.7706 (m-30) REVERT: B 456 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.5937 (tp) REVERT: B 462 LYS cc_start: 0.6827 (mptt) cc_final: 0.6200 (mttm) REVERT: C 189 LEU cc_start: 0.6329 (mp) cc_final: 0.6093 (mp) REVERT: C 287 ASP cc_start: 0.8580 (t0) cc_final: 0.8308 (t0) REVERT: C 291 CYS cc_start: 0.7560 (OUTLIER) cc_final: 0.7188 (m) REVERT: C 462 LYS cc_start: 0.7195 (mtpt) cc_final: 0.6412 (mptt) REVERT: C 467 ASP cc_start: 0.7378 (t0) cc_final: 0.6992 (t70) REVERT: C 537 LYS cc_start: 0.7291 (mtmm) cc_final: 0.6734 (mtpp) REVERT: C 902 MET cc_start: 0.8986 (mmm) cc_final: 0.8675 (mmt) REVERT: C 935 GLN cc_start: 0.7253 (tm130) cc_final: 0.6667 (tm-30) REVERT: C 950 ASP cc_start: 0.8386 (m-30) cc_final: 0.8160 (m-30) REVERT: C 1138 TYR cc_start: 0.7865 (t80) cc_final: 0.7435 (t80) outliers start: 52 outliers final: 38 residues processed: 242 average time/residue: 0.3632 time to fit residues: 140.1850 Evaluate side-chains 238 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 210 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 287 optimal weight: 0.7980 chunk 260 optimal weight: 2.9990 chunk 262 optimal weight: 0.3980 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 519 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.173657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.106023 restraints weight = 26601.970| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.38 r_work: 0.2876 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25605 Z= 0.126 Angle : 0.507 8.162 34928 Z= 0.261 Chirality : 0.044 0.246 4069 Planarity : 0.003 0.047 4436 Dihedral : 5.165 52.236 4203 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.03 % Allowed : 9.87 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.00 (0.15), residues: 3081 helix: 1.91 (0.20), residues: 723 sheet: 0.52 (0.19), residues: 674 loop : -1.12 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.006 0.001 HIS A 519 PHE 0.022 0.001 PHE C 565 TYR 0.014 0.001 TYR B1067 ARG 0.006 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 35) link_NAG-ASN : angle 1.57111 ( 105) link_BETA1-4 : bond 0.00377 ( 6) link_BETA1-4 : angle 1.12015 ( 18) hydrogen bonds : bond 0.04769 ( 959) hydrogen bonds : angle 4.66877 ( 2658) SS BOND : bond 0.00292 ( 42) SS BOND : angle 1.55289 ( 84) covalent geometry : bond 0.00302 (25522) covalent geometry : angle 0.49451 (34721) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 204 time to evaluate : 2.567 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6116 (OUTLIER) cc_final: 0.5810 (tt) REVERT: A 361 CYS cc_start: 0.7501 (p) cc_final: 0.7028 (p) REVERT: B 237 ARG cc_start: 0.7238 (mtp85) cc_final: 0.6984 (mtp85) REVERT: B 332 ILE cc_start: 0.8009 (pt) cc_final: 0.7671 (mt) REVERT: B 420 ASP cc_start: 0.8173 (m-30) cc_final: 0.7704 (m-30) REVERT: B 456 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.5808 (tp) REVERT: B 462 LYS cc_start: 0.6868 (mptt) cc_final: 0.6249 (mttm) REVERT: C 118 LEU cc_start: 0.6784 (tt) cc_final: 0.6561 (tt) REVERT: C 189 LEU cc_start: 0.6352 (mp) cc_final: 0.6067 (mp) REVERT: C 287 ASP cc_start: 0.8570 (t0) cc_final: 0.8283 (t0) REVERT: C 291 CYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7132 (m) REVERT: C 462 LYS cc_start: 0.7419 (mtpt) cc_final: 0.6510 (mptt) REVERT: C 467 ASP cc_start: 0.7409 (t0) cc_final: 0.7033 (t70) REVERT: C 537 LYS cc_start: 0.7324 (mtmm) cc_final: 0.6766 (mtpp) REVERT: C 902 MET cc_start: 0.8989 (mmm) cc_final: 0.8676 (mmt) REVERT: C 935 GLN cc_start: 0.7244 (tm130) cc_final: 0.6649 (tm-30) REVERT: C 950 ASP cc_start: 0.8366 (m-30) cc_final: 0.8137 (m-30) REVERT: C 1138 TYR cc_start: 0.7935 (t80) cc_final: 0.7514 (t80) outliers start: 55 outliers final: 43 residues processed: 245 average time/residue: 0.3533 time to fit residues: 138.2768 Evaluate side-chains 240 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 176 optimal weight: 0.0020 chunk 192 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 77 optimal weight: 0.4980 chunk 113 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 301 optimal weight: 0.0870 chunk 56 optimal weight: 0.9980 overall best weight: 0.5166 ------------------------------------------------------------------------------- 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 519 HIS A 613 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.174680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.110583 restraints weight = 26625.089| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.52 r_work: 0.2883 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25605 Z= 0.097 Angle : 0.498 12.241 34928 Z= 0.257 Chirality : 0.043 0.232 4069 Planarity : 0.003 0.046 4436 Dihedral : 4.990 52.888 4203 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.58 % Allowed : 10.53 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3081 helix: 1.94 (0.20), residues: 737 sheet: 0.59 (0.19), residues: 675 loop : -0.99 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.006 0.001 HIS A 519 PHE 0.021 0.001 PHE C 565 TYR 0.014 0.001 TYR B1067 ARG 0.006 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 35) link_NAG-ASN : angle 1.49499 ( 105) link_BETA1-4 : bond 0.00431 ( 6) link_BETA1-4 : angle 1.07824 ( 18) hydrogen bonds : bond 0.04266 ( 959) hydrogen bonds : angle 4.55527 ( 2658) SS BOND : bond 0.00258 ( 42) SS BOND : angle 2.05026 ( 84) covalent geometry : bond 0.00217 (25522) covalent geometry : angle 0.48168 (34721) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 2.648 Fit side-chains revert: symmetry clash REVERT: A 105 ILE cc_start: 0.7269 (pt) cc_final: 0.6885 (mt) REVERT: A 117 LEU cc_start: 0.5918 (OUTLIER) cc_final: 0.5587 (tt) REVERT: A 361 CYS cc_start: 0.7485 (p) cc_final: 0.7005 (p) REVERT: B 237 ARG cc_start: 0.7283 (mtp85) cc_final: 0.7041 (mtp85) REVERT: B 332 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7672 (mt) REVERT: B 420 ASP cc_start: 0.8207 (m-30) cc_final: 0.7744 (m-30) REVERT: B 456 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.5751 (tp) REVERT: C 118 LEU cc_start: 0.6809 (tt) cc_final: 0.6606 (tt) REVERT: C 189 LEU cc_start: 0.6219 (mp) cc_final: 0.5953 (mp) REVERT: C 287 ASP cc_start: 0.8604 (t0) cc_final: 0.8343 (t0) REVERT: C 291 CYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7081 (m) REVERT: C 462 LYS cc_start: 0.7448 (mtpt) cc_final: 0.6542 (mptt) REVERT: C 467 ASP cc_start: 0.7413 (t0) cc_final: 0.7042 (t70) REVERT: C 882 ILE cc_start: 0.8884 (mt) cc_final: 0.8553 (mm) REVERT: C 902 MET cc_start: 0.9030 (mmm) cc_final: 0.8720 (mmt) REVERT: C 935 GLN cc_start: 0.7281 (tm130) cc_final: 0.6696 (tm-30) REVERT: C 950 ASP cc_start: 0.8401 (m-30) cc_final: 0.8172 (m-30) REVERT: C 1138 TYR cc_start: 0.7978 (t80) cc_final: 0.7558 (t80) outliers start: 43 outliers final: 34 residues processed: 225 average time/residue: 0.3477 time to fit residues: 125.7285 Evaluate side-chains 230 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 154 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 238 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.174041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.107443 restraints weight = 26686.428| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.63 r_work: 0.2872 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25605 Z= 0.118 Angle : 0.510 11.386 34928 Z= 0.262 Chirality : 0.044 0.238 4069 Planarity : 0.003 0.048 4436 Dihedral : 4.970 52.101 4203 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.69 % Allowed : 11.01 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3081 helix: 2.07 (0.20), residues: 723 sheet: 0.60 (0.19), residues: 660 loop : -1.02 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.005 0.001 HIS A 519 PHE 0.022 0.001 PHE C 565 TYR 0.014 0.001 TYR C1067 ARG 0.013 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 35) link_NAG-ASN : angle 1.53459 ( 105) link_BETA1-4 : bond 0.00403 ( 6) link_BETA1-4 : angle 1.09453 ( 18) hydrogen bonds : bond 0.04584 ( 959) hydrogen bonds : angle 4.57622 ( 2658) SS BOND : bond 0.00264 ( 42) SS BOND : angle 1.98951 ( 84) covalent geometry : bond 0.00281 (25522) covalent geometry : angle 0.49422 (34721) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 2.761 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5708 (tt) REVERT: A 361 CYS cc_start: 0.7411 (p) cc_final: 0.6949 (p) REVERT: B 237 ARG cc_start: 0.7205 (mtp85) cc_final: 0.6942 (mtp85) REVERT: B 332 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7641 (mt) REVERT: B 456 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.5715 (tp) REVERT: C 189 LEU cc_start: 0.6209 (mp) cc_final: 0.5951 (mp) REVERT: C 287 ASP cc_start: 0.8641 (t0) cc_final: 0.8340 (t0) REVERT: C 291 CYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7191 (m) REVERT: C 462 LYS cc_start: 0.7372 (mtpt) cc_final: 0.6476 (mptt) REVERT: C 467 ASP cc_start: 0.7412 (t0) cc_final: 0.7045 (t70) REVERT: C 537 LYS cc_start: 0.7257 (mtmm) cc_final: 0.6698 (mtpp) REVERT: C 902 MET cc_start: 0.9001 (mmm) cc_final: 0.8673 (mmt) REVERT: C 935 GLN cc_start: 0.7234 (tm130) cc_final: 0.6628 (tm-30) REVERT: C 950 ASP cc_start: 0.8340 (m-30) cc_final: 0.8106 (m-30) REVERT: C 955 ASN cc_start: 0.7794 (m110) cc_final: 0.7585 (m110) REVERT: C 1138 TYR cc_start: 0.7894 (t80) cc_final: 0.7468 (t80) outliers start: 46 outliers final: 37 residues processed: 230 average time/residue: 0.3535 time to fit residues: 130.7167 Evaluate side-chains 231 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 178 optimal weight: 4.9990 chunk 270 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 269 optimal weight: 0.0170 chunk 34 optimal weight: 6.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 804 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 935 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.173642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.110272 restraints weight = 26596.238| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.63 r_work: 0.2838 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25605 Z= 0.120 Angle : 0.509 10.153 34928 Z= 0.262 Chirality : 0.044 0.241 4069 Planarity : 0.003 0.056 4436 Dihedral : 4.949 52.042 4203 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.73 % Allowed : 10.76 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3081 helix: 2.07 (0.20), residues: 720 sheet: 0.58 (0.19), residues: 675 loop : -1.02 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 64 HIS 0.005 0.001 HIS A 519 PHE 0.021 0.001 PHE C 565 TYR 0.014 0.001 TYR B1067 ARG 0.014 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 35) link_NAG-ASN : angle 1.53516 ( 105) link_BETA1-4 : bond 0.00370 ( 6) link_BETA1-4 : angle 1.08261 ( 18) hydrogen bonds : bond 0.04609 ( 959) hydrogen bonds : angle 4.55908 ( 2658) SS BOND : bond 0.00270 ( 42) SS BOND : angle 1.98867 ( 84) covalent geometry : bond 0.00285 (25522) covalent geometry : angle 0.49320 (34721) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 2.495 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5612 (tt) REVERT: A 237 ARG cc_start: 0.7534 (mpt-90) cc_final: 0.6351 (mtp-110) REVERT: A 361 CYS cc_start: 0.7249 (p) cc_final: 0.6785 (p) REVERT: B 237 ARG cc_start: 0.7165 (mtp85) cc_final: 0.6905 (mtp85) REVERT: B 332 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7674 (mt) REVERT: B 456 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.5750 (tp) REVERT: B 462 LYS cc_start: 0.6795 (mptt) cc_final: 0.6201 (mttm) REVERT: B 977 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7640 (mp) REVERT: C 189 LEU cc_start: 0.6364 (mp) cc_final: 0.6151 (mp) REVERT: C 287 ASP cc_start: 0.8542 (t0) cc_final: 0.8255 (t0) REVERT: C 462 LYS cc_start: 0.7425 (mtpt) cc_final: 0.6512 (mptt) REVERT: C 467 ASP cc_start: 0.7403 (t0) cc_final: 0.7040 (t70) REVERT: C 537 LYS cc_start: 0.7276 (mtmm) cc_final: 0.6721 (mtpp) REVERT: C 902 MET cc_start: 0.8908 (mmm) cc_final: 0.8569 (mmt) REVERT: C 935 GLN cc_start: 0.7241 (tm130) cc_final: 0.6643 (tm-30) REVERT: C 950 ASP cc_start: 0.8172 (m-30) cc_final: 0.7931 (m-30) REVERT: C 1138 TYR cc_start: 0.7964 (t80) cc_final: 0.7554 (t80) outliers start: 47 outliers final: 39 residues processed: 227 average time/residue: 0.3592 time to fit residues: 130.7537 Evaluate side-chains 231 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 278 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 204 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 172 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 519 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.175810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.109075 restraints weight = 26497.957| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.34 r_work: 0.2896 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25605 Z= 0.113 Angle : 0.509 9.736 34928 Z= 0.262 Chirality : 0.043 0.249 4069 Planarity : 0.003 0.058 4436 Dihedral : 4.915 52.301 4203 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.62 % Allowed : 11.01 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.17 (0.15), residues: 3081 helix: 2.10 (0.20), residues: 720 sheet: 0.53 (0.19), residues: 689 loop : -1.00 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.005 0.001 HIS A 519 PHE 0.022 0.001 PHE C 565 TYR 0.014 0.001 TYR C1067 ARG 0.014 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 35) link_NAG-ASN : angle 1.52146 ( 105) link_BETA1-4 : bond 0.00403 ( 6) link_BETA1-4 : angle 1.08238 ( 18) hydrogen bonds : bond 0.04493 ( 959) hydrogen bonds : angle 4.55011 ( 2658) SS BOND : bond 0.00279 ( 42) SS BOND : angle 2.23821 ( 84) covalent geometry : bond 0.00266 (25522) covalent geometry : angle 0.49042 (34721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15149.59 seconds wall clock time: 261 minutes 47.37 seconds (15707.37 seconds total)