Starting phenix.real_space_refine on Mon Aug 25 03:56:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0w_42872/08_2025/8v0w_42872.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0w_42872/08_2025/8v0w_42872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v0w_42872/08_2025/8v0w_42872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0w_42872/08_2025/8v0w_42872.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0w_42872/08_2025/8v0w_42872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0w_42872/08_2025/8v0w_42872.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24964 Number of models: 1 Model: "" Number of chains: 12 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: "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: "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: "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: "C" 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: "A" 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: 4.60, per 1000 atoms: 0.18 Number of scatterers: 24964 At special positions: 0 Unit cell: (138.24, 129.6, 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=41, symmetry=0 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 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 A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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 234 " " NAG A1310 " - " 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 801 " " NAG D 1 " - " ASN C 717 " " NAG E 1 " - " ASN C1098 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A1098 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 66 helices and 51 sheets defined 25.0% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.605A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.062A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.768A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 387' Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.927A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (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: 3.778A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.639A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 848 through 856 removed outlier: 4.036A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.556A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.511A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.690A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.775A 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: 3.752A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.750A 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 removed outlier: 3.507A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.544A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.421A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.777A pdb=" N ASN B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 4.216A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.689A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 411 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.845A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.563A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) 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: 3.827A 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: 3.616A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.594A 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 897 through 909 removed outlier: 3.527A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.979A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.784A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.547A 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 removed outlier: 3.602A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.527A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.150A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 4.322A pdb=" N ASN A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.887A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) 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: 3.695A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.625A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 842 removed outlier: 3.713A pdb=" N GLY A 842 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.566A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.516A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.761A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.741A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.700A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 Processing helix chain 'A' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'C' and resid 25 through 30 removed outlier: 3.644A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 25 through 30 removed outlier: 3.644A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 53 removed outlier: 3.759A pdb=" N LEU C 276 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.802A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.725A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 324 through 326 removed outlier: 3.545A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP C 586 " --> pdb=" O THR C 553 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.677A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.869A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'C' and resid 565 through 566 removed outlier: 6.760A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.939A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 701 through 703 removed outlier: 6.634A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AB6, first strand: chain 'C' and resid 718 through 722 removed outlier: 5.970A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.627A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.555A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.006A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.646A pdb=" N ARG A 567 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.973A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 101 through 104 removed outlier: 4.227A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.657A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 201 through 202 Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.398A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.534A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP B 586 " --> pdb=" O THR B 553 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.593A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.998A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.819A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.591A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 789 removed outlier: 5.849A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.234A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.822A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AE5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AE6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.241A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.566A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.816A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AF2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.157A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.635A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.594A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.640A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 1081 through 1083 870 hydrogen bonds defined for protein. 2373 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: 4.78 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6950 1.33 - 1.46: 6472 1.46 - 1.59: 11959 1.59 - 1.71: 0 1.71 - 1.84: 141 Bond restraints: 25522 Sorted by residual: bond pdb=" CG PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 1.503 1.208 0.295 3.40e-02 8.65e+02 7.50e+01 bond pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 1.332 1.398 -0.067 1.32e-02 5.74e+03 2.55e+01 bond pdb=" C GLN B1142 " pdb=" N PRO B1143 " ideal model delta sigma weight residual 1.336 1.378 -0.042 1.23e-02 6.61e+03 1.19e+01 bond pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.36e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 7.99e+00 ... (remaining 25517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 34428 3.54 - 7.09: 252 7.09 - 10.63: 33 10.63 - 14.18: 4 14.18 - 17.72: 4 Bond angle restraints: 34721 Sorted by residual: angle pdb=" N PRO A 384 " pdb=" CD PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 103.20 85.48 17.72 1.50e+00 4.44e-01 1.40e+02 angle pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 112.00 96.65 15.35 1.40e+00 5.10e-01 1.20e+02 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 128.70 -14.30 2.30e+00 1.89e-01 3.86e+01 angle pdb=" CA PRO A 384 " pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 104.50 93.00 11.50 1.90e+00 2.77e-01 3.66e+01 angle pdb=" C VAL C1040 " pdb=" N ASP C1041 " pdb=" CA ASP C1041 " ideal model delta sigma weight residual 121.54 132.26 -10.72 1.91e+00 2.74e-01 3.15e+01 ... (remaining 34716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 14184 17.93 - 35.86: 1283 35.86 - 53.80: 206 53.80 - 71.73: 70 71.73 - 89.66: 34 Dihedral angle restraints: 15777 sinusoidal: 6672 harmonic: 9105 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 1.35 -87.35 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 6.77 86.23 1 1.00e+01 1.00e-02 8.97e+01 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 -86.00 -171.40 85.40 1 1.00e+01 1.00e-02 8.83e+01 ... (remaining 15774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 4010 0.151 - 0.301: 54 0.301 - 0.452: 3 0.452 - 0.602: 1 0.602 - 0.753: 1 Chirality restraints: 4069 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CB ILE B 203 " pdb=" CA ILE B 203 " pdb=" CG1 ILE B 203 " pdb=" CG2 ILE B 203 " both_signs ideal model delta sigma weight residual False 2.64 3.09 -0.45 2.00e-01 2.50e+01 5.04e+00 ... (remaining 4066 not shown) Planarity restraints: 4471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " 0.106 5.00e-02 4.00e+02 1.47e-01 3.45e+01 pdb=" N PRO A 384 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 203 " -0.021 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ILE B 203 " 0.071 2.00e-02 2.50e+03 pdb=" O ILE B 203 " -0.027 2.00e-02 2.50e+03 pdb=" N TYR B 204 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 91 " 0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C TYR C 91 " -0.065 2.00e-02 2.50e+03 pdb=" O TYR C 91 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE C 92 " 0.022 2.00e-02 2.50e+03 ... (remaining 4468 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3983 2.77 - 3.30: 21167 3.30 - 3.83: 39857 3.83 - 4.37: 44378 4.37 - 4.90: 80242 Nonbonded interactions: 189627 Sorted by model distance: nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.236 3.040 nonbonded pdb=" OG SER C 438 " pdb=" O PRO C 507 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR B1100 " pdb=" O7 NAG G 1 " model vdw 2.307 3.040 nonbonded pdb=" OH TYR B 200 " pdb=" OE2 GLU A 516 " model vdw 2.309 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.322 3.040 ... (remaining 189622 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' and resid 24 through 1309) selection = (chain 'B' and resid 24 through 1309) selection = chain 'C' } 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.160 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 : 0.005 0.295 25604 Z= 0.247 Angle : 0.895 18.694 34926 Z= 0.472 Chirality : 0.058 0.753 4069 Planarity : 0.007 0.147 4436 Dihedral : 14.319 89.661 9792 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.76 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.14), residues: 3081 helix: -0.53 (0.17), residues: 673 sheet: -0.03 (0.21), residues: 585 loop : -2.09 (0.13), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 190 TYR 0.037 0.002 TYR B 904 PHE 0.048 0.003 PHE C 541 TRP 0.018 0.002 TRP B 886 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00534 (25522) covalent geometry : angle 0.86865 (34721) SS BOND : bond 0.00538 ( 41) SS BOND : angle 2.15628 ( 82) hydrogen bonds : bond 0.20689 ( 853) hydrogen bonds : angle 7.71913 ( 2373) link_BETA1-4 : bond 0.00756 ( 6) link_BETA1-4 : angle 1.86405 ( 18) link_NAG-ASN : bond 0.00771 ( 35) link_NAG-ASN : angle 3.57434 ( 105) *********************** 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 220 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 309 GLU cc_start: 0.7360 (mp0) cc_final: 0.7041 (mp0) REVERT: C 356 LYS cc_start: 0.7673 (tptp) cc_final: 0.7450 (tmtt) REVERT: B 168 PHE cc_start: 0.8137 (t80) cc_final: 0.7814 (t80) REVERT: A 1138 TYR cc_start: 0.7761 (t80) cc_final: 0.7060 (t80) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1319 time to fit residues: 47.4908 Evaluate side-chains 174 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.0050 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.0010 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.5980 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 GLN C 437 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 493 GLN A 218 GLN A 239 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.201482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.3438 r_free = 0.3438 target = 0.132315 restraints weight = 29158.588| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.13 r_work: 0.3050 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25604 Z= 0.108 Angle : 0.573 13.620 34926 Z= 0.296 Chirality : 0.044 0.401 4069 Planarity : 0.004 0.044 4436 Dihedral : 6.431 59.154 4203 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.26 % Favored : 93.70 % Rotamer: Outliers : 0.48 % Allowed : 4.83 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.14), residues: 3081 helix: 1.06 (0.20), residues: 682 sheet: 0.06 (0.22), residues: 572 loop : -1.86 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.021 0.001 TYR B 170 PHE 0.020 0.001 PHE A 541 TRP 0.011 0.001 TRP C 886 HIS 0.003 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00234 (25522) covalent geometry : angle 0.55429 (34721) SS BOND : bond 0.00272 ( 41) SS BOND : angle 1.49125 ( 82) hydrogen bonds : bond 0.04826 ( 853) hydrogen bonds : angle 5.51613 ( 2373) link_BETA1-4 : bond 0.00298 ( 6) link_BETA1-4 : angle 1.29441 ( 18) link_NAG-ASN : bond 0.00477 ( 35) link_NAG-ASN : angle 2.36384 ( 105) *********************** 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 203 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 356 LYS cc_start: 0.7293 (tptp) cc_final: 0.7083 (tppt) REVERT: C 581 THR cc_start: 0.7984 (m) cc_final: 0.7190 (p) REVERT: C 583 GLU cc_start: 0.7427 (pm20) cc_final: 0.6984 (pm20) REVERT: B 1138 TYR cc_start: 0.7947 (t80) cc_final: 0.7735 (t80) REVERT: A 32 PHE cc_start: 0.7619 (m-80) cc_final: 0.7216 (m-80) REVERT: A 226 LEU cc_start: 0.8374 (tt) cc_final: 0.8152 (tt) REVERT: A 237 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7376 (mtm-85) REVERT: A 820 ASP cc_start: 0.8028 (t0) cc_final: 0.7690 (t0) REVERT: A 923 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8252 (mp) REVERT: A 1138 TYR cc_start: 0.8144 (t80) cc_final: 0.7474 (t80) outliers start: 13 outliers final: 8 residues processed: 197 average time/residue: 0.1332 time to fit residues: 42.6171 Evaluate side-chains 190 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 181 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 923 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 182 optimal weight: 3.9990 chunk 266 optimal weight: 0.3980 chunk 134 optimal weight: 1.9990 chunk 289 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 173 optimal weight: 0.8980 chunk 280 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 HIS C 52 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 448 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 = 0.4187 r_free = 0.4187 target = 0.200293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.126499 restraints weight = 29496.696| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.80 r_work: 0.3036 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25604 Z= 0.103 Angle : 0.533 13.783 34926 Z= 0.273 Chirality : 0.044 0.373 4069 Planarity : 0.004 0.043 4436 Dihedral : 5.827 57.566 4203 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.33 % Favored : 93.64 % Rotamer: Outliers : 0.77 % Allowed : 7.70 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.15), residues: 3081 helix: 1.69 (0.20), residues: 677 sheet: 0.10 (0.21), residues: 585 loop : -1.75 (0.13), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 983 TYR 0.020 0.001 TYR B 170 PHE 0.022 0.001 PHE A 541 TRP 0.008 0.001 TRP C 886 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00234 (25522) covalent geometry : angle 0.51611 (34721) SS BOND : bond 0.00259 ( 41) SS BOND : angle 1.32633 ( 82) hydrogen bonds : bond 0.04288 ( 853) hydrogen bonds : angle 4.95706 ( 2373) link_BETA1-4 : bond 0.00341 ( 6) link_BETA1-4 : angle 1.13067 ( 18) link_NAG-ASN : bond 0.00432 ( 35) link_NAG-ASN : angle 2.17359 ( 105) *********************** 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 215 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 355 ARG cc_start: 0.8523 (ttm-80) cc_final: 0.8206 (ttm-80) REVERT: C 607 GLN cc_start: 0.8256 (mt0) cc_final: 0.7818 (mt0) REVERT: C 779 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8233 (tm-30) REVERT: B 200 TYR cc_start: 0.7235 (m-80) cc_final: 0.6911 (m-80) REVERT: B 931 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.7088 (tp) REVERT: B 1092 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8240 (pt0) REVERT: B 1138 TYR cc_start: 0.7697 (t80) cc_final: 0.7445 (t80) REVERT: A 32 PHE cc_start: 0.7728 (m-80) cc_final: 0.7237 (m-80) REVERT: A 226 LEU cc_start: 0.8351 (tt) cc_final: 0.8128 (tt) REVERT: A 237 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.7148 (mtm-85) REVERT: A 902 MET cc_start: 0.8991 (mmm) cc_final: 0.8710 (tpt) REVERT: A 1138 TYR cc_start: 0.7925 (t80) cc_final: 0.7337 (t80) outliers start: 21 outliers final: 11 residues processed: 203 average time/residue: 0.1545 time to fit residues: 51.3876 Evaluate side-chains 186 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 1101 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 55 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 264 optimal weight: 0.0010 chunk 265 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 297 optimal weight: 2.9990 chunk 307 optimal weight: 0.7980 chunk 224 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 chunk 278 optimal weight: 0.8980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN C 271 GLN C 437 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN A 360 ASN A 564 GLN A 613 GLN A 804 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.199789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.125507 restraints weight = 29420.801| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.96 r_work: 0.3077 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25604 Z= 0.102 Angle : 0.517 12.927 34926 Z= 0.265 Chirality : 0.043 0.365 4069 Planarity : 0.003 0.043 4436 Dihedral : 5.522 57.563 4203 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.93 % Rotamer: Outliers : 0.81 % Allowed : 9.47 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.15), residues: 3081 helix: 1.93 (0.20), residues: 677 sheet: 0.14 (0.21), residues: 595 loop : -1.70 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.017 0.001 TYR B 170 PHE 0.022 0.001 PHE A 541 TRP 0.008 0.001 TRP B 886 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00235 (25522) covalent geometry : angle 0.49853 (34721) SS BOND : bond 0.00253 ( 41) SS BOND : angle 1.32372 ( 82) hydrogen bonds : bond 0.04132 ( 853) hydrogen bonds : angle 4.69912 ( 2373) link_BETA1-4 : bond 0.00325 ( 6) link_BETA1-4 : angle 1.08199 ( 18) link_NAG-ASN : bond 0.00417 ( 35) link_NAG-ASN : angle 2.26241 ( 105) *********************** 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 208 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 533 LEU cc_start: 0.8169 (tp) cc_final: 0.7957 (tt) REVERT: B 200 TYR cc_start: 0.7106 (m-80) cc_final: 0.6787 (m-80) REVERT: B 1092 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8124 (pt0) REVERT: B 1138 TYR cc_start: 0.7964 (t80) cc_final: 0.7695 (t80) REVERT: A 32 PHE cc_start: 0.7810 (m-80) cc_final: 0.7322 (m-80) REVERT: A 53 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7159 (t70) REVERT: A 226 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8163 (tt) REVERT: A 237 ARG cc_start: 0.7694 (mtm-85) cc_final: 0.7385 (mtp180) REVERT: A 902 MET cc_start: 0.8913 (mmm) cc_final: 0.8704 (tpt) REVERT: A 1138 TYR cc_start: 0.8182 (t80) cc_final: 0.7579 (t80) outliers start: 22 outliers final: 11 residues processed: 200 average time/residue: 0.1538 time to fit residues: 50.3310 Evaluate side-chains 184 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 676 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 223 optimal weight: 0.1980 chunk 294 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 310 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 chunk 272 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN A 564 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.200046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.152253 restraints weight = 29009.633| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.08 r_work: 0.3020 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25604 Z= 0.134 Angle : 0.536 13.729 34926 Z= 0.274 Chirality : 0.045 0.487 4069 Planarity : 0.004 0.042 4436 Dihedral : 5.412 58.217 4203 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.43 % Favored : 93.54 % Rotamer: Outliers : 1.10 % Allowed : 10.64 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.15), residues: 3081 helix: 1.91 (0.20), residues: 675 sheet: 0.15 (0.21), residues: 591 loop : -1.71 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.016 0.001 TYR B 904 PHE 0.021 0.001 PHE A 541 TRP 0.011 0.001 TRP B 886 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00325 (25522) covalent geometry : angle 0.51735 (34721) SS BOND : bond 0.00280 ( 41) SS BOND : angle 1.43198 ( 82) hydrogen bonds : bond 0.04599 ( 853) hydrogen bonds : angle 4.67055 ( 2373) link_BETA1-4 : bond 0.00287 ( 6) link_BETA1-4 : angle 1.12053 ( 18) link_NAG-ASN : bond 0.00397 ( 35) link_NAG-ASN : angle 2.32013 ( 105) *********************** 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 214 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 607 GLN cc_start: 0.8262 (mt0) cc_final: 0.8038 (mt0) REVERT: B 52 GLN cc_start: 0.8498 (tm-30) cc_final: 0.7955 (tm-30) REVERT: B 200 TYR cc_start: 0.7168 (m-80) cc_final: 0.6933 (m-80) REVERT: B 1138 TYR cc_start: 0.8160 (t80) cc_final: 0.7888 (t80) REVERT: A 32 PHE cc_start: 0.7974 (m-80) cc_final: 0.7414 (m-80) REVERT: A 53 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7363 (t70) REVERT: A 226 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8159 (tt) REVERT: A 237 ARG cc_start: 0.7891 (mtm-85) cc_final: 0.7557 (mtp180) REVERT: A 1029 MET cc_start: 0.9028 (tpp) cc_final: 0.8612 (ttm) REVERT: A 1138 TYR cc_start: 0.8310 (t80) cc_final: 0.7758 (t80) outliers start: 30 outliers final: 16 residues processed: 207 average time/residue: 0.1385 time to fit residues: 46.2942 Evaluate side-chains 194 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 59 optimal weight: 6.9990 chunk 290 optimal weight: 1.9990 chunk 131 optimal weight: 30.0000 chunk 149 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 176 optimal weight: 0.4980 chunk 117 optimal weight: 0.5980 chunk 255 optimal weight: 9.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 644 GLN C 872 GLN A 564 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.195138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.147561 restraints weight = 29011.127| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.05 r_work: 0.2953 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 25604 Z= 0.234 Angle : 0.635 14.296 34926 Z= 0.325 Chirality : 0.047 0.369 4069 Planarity : 0.004 0.042 4436 Dihedral : 5.802 59.810 4203 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.72 % Favored : 92.24 % Rotamer: Outliers : 1.66 % Allowed : 11.82 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.15), residues: 3081 helix: 1.57 (0.20), residues: 673 sheet: 0.03 (0.21), residues: 591 loop : -1.80 (0.13), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.019 0.002 TYR B 904 PHE 0.024 0.002 PHE B 906 TRP 0.011 0.001 TRP C 353 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00581 (25522) covalent geometry : angle 0.61357 (34721) SS BOND : bond 0.00404 ( 41) SS BOND : angle 1.87826 ( 82) hydrogen bonds : bond 0.06055 ( 853) hydrogen bonds : angle 4.90118 ( 2373) link_BETA1-4 : bond 0.00322 ( 6) link_BETA1-4 : angle 1.23903 ( 18) link_NAG-ASN : bond 0.00397 ( 35) link_NAG-ASN : angle 2.54817 ( 105) *********************** 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 229 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 LEU cc_start: 0.7184 (mt) cc_final: 0.6968 (mp) REVERT: B 237 ARG cc_start: 0.7891 (ttt90) cc_final: 0.7167 (ttm-80) REVERT: B 1138 TYR cc_start: 0.8303 (t80) cc_final: 0.8013 (t80) REVERT: A 32 PHE cc_start: 0.8023 (m-80) cc_final: 0.7425 (m-80) REVERT: A 226 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8353 (tt) REVERT: A 237 ARG cc_start: 0.7940 (mtm-85) cc_final: 0.7717 (mtm-85) REVERT: A 931 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8421 (tt) REVERT: A 1029 MET cc_start: 0.9093 (tpp) cc_final: 0.8769 (ttm) REVERT: A 1138 TYR cc_start: 0.8323 (t80) cc_final: 0.7812 (t80) outliers start: 45 outliers final: 26 residues processed: 216 average time/residue: 0.1479 time to fit residues: 52.0095 Evaluate side-chains 203 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 104 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 chunk 271 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 73 optimal weight: 0.4980 chunk 277 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN A 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.198310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.151089 restraints weight = 28800.745| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.10 r_work: 0.2996 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25604 Z= 0.115 Angle : 0.548 13.711 34926 Z= 0.280 Chirality : 0.044 0.354 4069 Planarity : 0.003 0.042 4436 Dihedral : 5.459 58.376 4203 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.23 % Favored : 93.74 % Rotamer: Outliers : 1.36 % Allowed : 12.56 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.15), residues: 3081 helix: 1.97 (0.21), residues: 665 sheet: 0.04 (0.21), residues: 591 loop : -1.71 (0.13), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.016 0.001 TYR B 904 PHE 0.024 0.001 PHE A 392 TRP 0.009 0.001 TRP C 353 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00269 (25522) covalent geometry : angle 0.52809 (34721) SS BOND : bond 0.00294 ( 41) SS BOND : angle 1.68347 ( 82) hydrogen bonds : bond 0.04746 ( 853) hydrogen bonds : angle 4.66901 ( 2373) link_BETA1-4 : bond 0.00330 ( 6) link_BETA1-4 : angle 1.16828 ( 18) link_NAG-ASN : bond 0.00410 ( 35) link_NAG-ASN : angle 2.30432 ( 105) *********************** 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 212 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ARG cc_start: 0.7913 (ttp-110) cc_final: 0.7488 (ptp-110) REVERT: C 53 ASP cc_start: 0.6374 (t70) cc_final: 0.6139 (t70) REVERT: C 204 TYR cc_start: 0.7158 (m-80) cc_final: 0.6603 (m-80) REVERT: C 396 TYR cc_start: 0.7973 (m-80) cc_final: 0.7754 (m-10) REVERT: C 607 GLN cc_start: 0.8316 (mt0) cc_final: 0.8113 (mt0) REVERT: B 237 ARG cc_start: 0.7857 (ttt90) cc_final: 0.7201 (ttm-80) REVERT: B 1138 TYR cc_start: 0.8195 (t80) cc_final: 0.7902 (t80) REVERT: A 32 PHE cc_start: 0.8060 (m-80) cc_final: 0.7312 (m-80) REVERT: A 53 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7524 (t70) REVERT: A 226 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8303 (tt) REVERT: A 237 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7403 (mtp85) REVERT: A 1138 TYR cc_start: 0.8388 (t80) cc_final: 0.7801 (t80) outliers start: 37 outliers final: 23 residues processed: 206 average time/residue: 0.1457 time to fit residues: 48.8946 Evaluate side-chains 194 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 294 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 247 optimal weight: 20.0000 chunk 242 optimal weight: 0.8980 chunk 201 optimal weight: 0.0570 chunk 140 optimal weight: 20.0000 chunk 224 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.196921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.154039 restraints weight = 28941.136| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.93 r_work: 0.3008 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25604 Z= 0.156 Angle : 0.569 14.024 34926 Z= 0.289 Chirality : 0.045 0.354 4069 Planarity : 0.004 0.048 4436 Dihedral : 5.464 59.194 4203 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.04 % Favored : 92.92 % Rotamer: Outliers : 1.51 % Allowed : 12.97 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.15), residues: 3081 helix: 1.89 (0.20), residues: 666 sheet: -0.01 (0.21), residues: 592 loop : -1.71 (0.13), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.017 0.001 TYR B 904 PHE 0.020 0.001 PHE A 392 TRP 0.011 0.001 TRP C 353 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00383 (25522) covalent geometry : angle 0.54835 (34721) SS BOND : bond 0.00324 ( 41) SS BOND : angle 1.68947 ( 82) hydrogen bonds : bond 0.05079 ( 853) hydrogen bonds : angle 4.67812 ( 2373) link_BETA1-4 : bond 0.00312 ( 6) link_BETA1-4 : angle 1.17314 ( 18) link_NAG-ASN : bond 0.00384 ( 35) link_NAG-ASN : angle 2.39044 ( 105) *********************** 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 214 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7508 (ptp-110) REVERT: B 237 ARG cc_start: 0.7972 (ttt90) cc_final: 0.7349 (ttm-80) REVERT: B 1138 TYR cc_start: 0.8248 (t80) cc_final: 0.7950 (t80) REVERT: A 32 PHE cc_start: 0.8091 (m-80) cc_final: 0.7283 (m-80) REVERT: A 226 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8274 (tt) REVERT: A 237 ARG cc_start: 0.7941 (mtm-85) cc_final: 0.7710 (mtm-85) REVERT: A 541 PHE cc_start: 0.7171 (p90) cc_final: 0.6906 (p90) REVERT: A 1138 TYR cc_start: 0.8364 (t80) cc_final: 0.7838 (t80) outliers start: 41 outliers final: 33 residues processed: 202 average time/residue: 0.1398 time to fit residues: 47.5472 Evaluate side-chains 203 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1083 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 236 optimal weight: 5.9990 chunk 225 optimal weight: 0.7980 chunk 212 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 177 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.196245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.143166 restraints weight = 28931.224| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.29 r_work: 0.3067 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25604 Z= 0.169 Angle : 0.575 14.191 34926 Z= 0.293 Chirality : 0.045 0.327 4069 Planarity : 0.004 0.059 4436 Dihedral : 5.501 59.165 4203 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.69 % Favored : 93.28 % Rotamer: Outliers : 1.51 % Allowed : 13.22 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.15), residues: 3081 helix: 1.86 (0.20), residues: 665 sheet: -0.03 (0.21), residues: 592 loop : -1.70 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.018 0.001 TYR B 904 PHE 0.022 0.002 PHE A 565 TRP 0.010 0.001 TRP A 353 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00418 (25522) covalent geometry : angle 0.55517 (34721) SS BOND : bond 0.00348 ( 41) SS BOND : angle 1.72976 ( 82) hydrogen bonds : bond 0.05211 ( 853) hydrogen bonds : angle 4.69693 ( 2373) link_BETA1-4 : bond 0.00273 ( 6) link_BETA1-4 : angle 1.18347 ( 18) link_NAG-ASN : bond 0.00337 ( 35) link_NAG-ASN : angle 2.36368 ( 105) *********************** 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 215 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ARG cc_start: 0.7909 (ttp-110) cc_final: 0.7518 (ptp-110) REVERT: B 237 ARG cc_start: 0.8012 (ttt90) cc_final: 0.7453 (ttm-80) REVERT: B 1138 TYR cc_start: 0.8348 (t80) cc_final: 0.8070 (t80) REVERT: A 32 PHE cc_start: 0.8094 (m-80) cc_final: 0.7267 (m-80) REVERT: A 237 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7753 (mtm-85) REVERT: A 541 PHE cc_start: 0.7493 (p90) cc_final: 0.7282 (p90) REVERT: A 1138 TYR cc_start: 0.8370 (t80) cc_final: 0.7915 (t80) outliers start: 41 outliers final: 34 residues processed: 205 average time/residue: 0.1322 time to fit residues: 45.0300 Evaluate side-chains 206 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1083 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 305 optimal weight: 0.9990 chunk 214 optimal weight: 9.9990 chunk 232 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 283 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 chunk 310 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN A 564 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.198484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.152356 restraints weight = 28883.204| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.97 r_work: 0.3223 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25604 Z= 0.115 Angle : 0.553 13.500 34926 Z= 0.278 Chirality : 0.044 0.324 4069 Planarity : 0.004 0.048 4436 Dihedral : 5.334 58.152 4203 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.52 % Favored : 93.44 % Rotamer: Outliers : 1.18 % Allowed : 13.96 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.15), residues: 3081 helix: 2.05 (0.20), residues: 665 sheet: 0.05 (0.21), residues: 592 loop : -1.64 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.017 0.001 TYR B 904 PHE 0.018 0.001 PHE A 392 TRP 0.013 0.001 TRP A 353 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00271 (25522) covalent geometry : angle 0.53495 (34721) SS BOND : bond 0.00286 ( 41) SS BOND : angle 1.58178 ( 82) hydrogen bonds : bond 0.04508 ( 853) hydrogen bonds : angle 4.58827 ( 2373) link_BETA1-4 : bond 0.00333 ( 6) link_BETA1-4 : angle 1.13338 ( 18) link_NAG-ASN : bond 0.00387 ( 35) link_NAG-ASN : angle 2.20103 ( 105) ********************** 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 206 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ARG cc_start: 0.7950 (ttp-110) cc_final: 0.7619 (ptp-110) REVERT: C 204 TYR cc_start: 0.7433 (m-80) cc_final: 0.6871 (m-80) REVERT: B 237 ARG cc_start: 0.7941 (ttt90) cc_final: 0.7519 (ttm-80) REVERT: B 1138 TYR cc_start: 0.8351 (t80) cc_final: 0.8126 (t80) REVERT: A 32 PHE cc_start: 0.8034 (m-80) cc_final: 0.7223 (m-80) REVERT: A 237 ARG cc_start: 0.7984 (mtm-85) cc_final: 0.7622 (mtp85) REVERT: A 531 THR cc_start: 0.7988 (m) cc_final: 0.7522 (p) REVERT: A 541 PHE cc_start: 0.7589 (p90) cc_final: 0.7372 (p90) REVERT: A 1138 TYR cc_start: 0.8439 (t80) cc_final: 0.8014 (t80) outliers start: 32 outliers final: 29 residues processed: 199 average time/residue: 0.1303 time to fit residues: 42.8563 Evaluate side-chains 196 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 175 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 chunk 249 optimal weight: 20.0000 chunk 176 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 257 optimal weight: 1.9990 chunk 278 optimal weight: 0.0570 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.198869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.152299 restraints weight = 28718.055| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.04 r_work: 0.3006 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25604 Z= 0.112 Angle : 0.556 13.581 34926 Z= 0.279 Chirality : 0.044 0.335 4069 Planarity : 0.004 0.047 4436 Dihedral : 5.269 57.904 4203 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.20 % Favored : 93.77 % Rotamer: Outliers : 1.29 % Allowed : 13.78 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.15), residues: 3081 helix: 2.13 (0.20), residues: 665 sheet: 0.05 (0.21), residues: 592 loop : -1.62 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.019 0.001 TYR B 904 PHE 0.020 0.001 PHE A 392 TRP 0.013 0.001 TRP A 353 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00258 (25522) covalent geometry : angle 0.53918 (34721) SS BOND : bond 0.00286 ( 41) SS BOND : angle 1.52816 ( 82) hydrogen bonds : bond 0.04384 ( 853) hydrogen bonds : angle 4.54716 ( 2373) link_BETA1-4 : bond 0.00340 ( 6) link_BETA1-4 : angle 1.11638 ( 18) link_NAG-ASN : bond 0.00393 ( 35) link_NAG-ASN : angle 2.17240 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6164.94 seconds wall clock time: 105 minutes 57.68 seconds (6357.68 seconds total)