Starting phenix.real_space_refine on Mon Aug 25 03:01:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0x_42873/08_2025/8v0x_42873.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0x_42873/08_2025/8v0x_42873.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 { model { file = "/net/cci-nas-00/data/ceres_data/8v0x_42873/08_2025/8v0x_42873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0x_42873/08_2025/8v0x_42873.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v0x_42873/08_2025/8v0x_42873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0x_42873/08_2025/8v0x_42873.map" } 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= 0.044 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 15829 2.51 5 N 4091 2.21 5 O 4762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s 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: 24796 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "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: "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: 5.44, per 1000 atoms: 0.22 Number of scatterers: 24796 At special positions: 0 Unit cell: (138.24, 132.84, 174.96, 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 4762 8.00 N 4091 7.00 C 15829 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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 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 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 796.4 milliseconds Enol-peptide restraints added in 953.7 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: 69 helices and 51 sheets defined 25.1% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.678A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 372' Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.149A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 4.104A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 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: 3.621A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.655A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 842 Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.601A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.605A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.662A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.913A 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: 3.586A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 4.046A 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: 3.555A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.873A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.824A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.614A 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: 3.794A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 836 through 842 Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.613A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.521A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 4.125A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.519A 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 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.888A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (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: 3.522A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.608A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.171A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.588A 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 349 through 353 removed outlier: 4.102A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.789A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (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: 3.564A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.509A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 842 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 891 removed outlier: 3.525A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.784A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.586A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.655A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.692A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.731A 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: 3.539A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.540A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) 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: 7.563A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.558A pdb=" N PHE C 43 " --> pdb=" O PHE B 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.636A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.084A 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 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 104 removed outlier: 4.171A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.364A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.007A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.956A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.173A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 701 through 704 removed outlier: 6.643A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LYS A 790 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASN C 703 " --> pdb=" O LYS A 790 " (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 722 removed outlier: 6.282A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.610A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 25 through 30 removed outlier: 4.308A pdb=" N THR B 25 " --> pdb=" O HIS B 66 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.912A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.672A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 224 through 229 removed outlier: 6.041A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 118 through 120 removed outlier: 3.536A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.379A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.554A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.506A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.887A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.613A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.196A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.526A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.397A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'A' and resid 25 through 29 removed outlier: 3.600A pdb=" N THR A 25 " --> pdb=" O HIS A 66 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ARG A 34 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N LEU A 223 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.558A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.558A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.577A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.759A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.369A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.628A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.699A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.086A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.519A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AF3, first strand: chain 'A' and resid 718 through 722 removed outlier: 7.155A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.374A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.525A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 1094 through 1097 887 hydrogen bonds defined for protein. 2466 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: 5.43 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7922 1.35 - 1.47: 6482 1.47 - 1.60: 10809 1.60 - 1.73: 0 1.73 - 1.86: 141 Bond restraints: 25354 Sorted by residual: bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C ALA C 520 " pdb=" N PRO C 521 " ideal model delta sigma weight residual 1.330 1.361 -0.031 1.23e-02 6.61e+03 6.26e+00 bond pdb=" C1 NAG C1309 " pdb=" O5 NAG C1309 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.42e+00 bond pdb=" N ASP C 745 " pdb=" CA ASP C 745 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.13e+00 ... (remaining 25349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 34075 2.87 - 5.73: 349 5.73 - 8.60: 53 8.60 - 11.47: 13 11.47 - 14.33: 3 Bond angle restraints: 34493 Sorted by residual: angle pdb=" N VAL C 130 " pdb=" CA VAL C 130 " pdb=" C VAL C 130 " ideal model delta sigma weight residual 111.77 102.62 9.15 1.04e+00 9.25e-01 7.73e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 121.54 131.86 -10.32 1.91e+00 2.74e-01 2.92e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 126.56 -12.16 2.30e+00 1.89e-01 2.79e+01 angle pdb=" CG1 ILE C 105 " pdb=" CB ILE C 105 " pdb=" CG2 ILE C 105 " ideal model delta sigma weight residual 110.70 96.37 14.33 3.00e+00 1.11e-01 2.28e+01 angle pdb=" C VAL C 130 " pdb=" CA VAL C 130 " pdb=" CB VAL C 130 " ideal model delta sigma weight residual 112.46 118.73 -6.27 1.33e+00 5.65e-01 2.22e+01 ... (remaining 34488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.66: 14504 23.66 - 47.33: 889 47.33 - 70.99: 95 70.99 - 94.65: 36 94.65 - 118.32: 1 Dihedral angle restraints: 15525 sinusoidal: 6420 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 93.00 9.36 83.64 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -4.19 -81.81 1 1.00e+01 1.00e-02 8.23e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -15.47 -70.53 1 1.00e+01 1.00e-02 6.40e+01 ... (remaining 15522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3402 0.075 - 0.150: 563 0.150 - 0.225: 40 0.225 - 0.300: 2 0.300 - 0.375: 2 Chirality restraints: 4009 Sorted by residual: chirality pdb=" CB ILE C 105 " pdb=" CA ILE C 105 " pdb=" CG1 ILE C 105 " pdb=" CG2 ILE C 105 " both_signs ideal model delta sigma weight residual False 2.64 3.02 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE A 101 " pdb=" CA ILE A 101 " pdb=" CG1 ILE A 101 " pdb=" CG2 ILE A 101 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE B 101 " pdb=" CA ILE B 101 " pdb=" CG1 ILE B 101 " pdb=" CG2 ILE B 101 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 4006 not shown) Planarity restraints: 4453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 138 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO B 139 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO B 139 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 139 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 105 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C ILE C 105 " -0.064 2.00e-02 2.50e+03 pdb=" O ILE C 105 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE C 106 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 173 " -0.048 5.00e-02 4.00e+02 7.24e-02 8.39e+00 pdb=" N PRO C 174 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 174 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 174 " -0.040 5.00e-02 4.00e+02 ... (remaining 4450 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7248 2.82 - 3.34: 19813 3.34 - 3.86: 39614 3.86 - 4.38: 42960 4.38 - 4.90: 78621 Nonbonded interactions: 188256 Sorted by model distance: nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.304 3.040 nonbonded pdb=" OE1 GLU A 819 " pdb=" OG SER A1055 " model vdw 2.316 3.040 nonbonded pdb=" O PHE C 374 " pdb=" ND2 ASN B 405 " model vdw 2.325 3.120 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.330 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.330 3.040 ... (remaining 188251 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' } 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.950 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 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 : 0.004 0.096 25424 Z= 0.207 Angle : 0.805 14.331 34662 Z= 0.418 Chirality : 0.052 0.375 4009 Planarity : 0.006 0.104 4424 Dihedral : 14.552 118.315 9540 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.76 (0.14), residues: 3081 helix: -0.60 (0.17), residues: 682 sheet: -0.19 (0.20), residues: 653 loop : -1.85 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 646 TYR 0.028 0.001 TYR B 170 PHE 0.047 0.002 PHE C 168 TRP 0.013 0.001 TRP C 886 HIS 0.013 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00422 (25354) covalent geometry : angle 0.79083 (34493) SS BOND : bond 0.00538 ( 41) SS BOND : angle 1.75621 ( 82) hydrogen bonds : bond 0.21040 ( 882) hydrogen bonds : angle 7.43664 ( 2466) link_NAG-ASN : bond 0.00468 ( 29) link_NAG-ASN : angle 2.76216 ( 87) *********************** 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 279 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 537 LYS cc_start: 0.6882 (mtpp) cc_final: 0.6597 (mttt) REVERT: C 544 ASN cc_start: 0.8754 (m-40) cc_final: 0.8518 (m-40) REVERT: B 303 LEU cc_start: 0.8676 (mt) cc_final: 0.8415 (mt) REVERT: A 287 ASP cc_start: 0.6692 (m-30) cc_final: 0.6464 (m-30) REVERT: A 392 PHE cc_start: 0.6883 (m-10) cc_final: 0.6558 (m-80) REVERT: A 904 TYR cc_start: 0.7220 (m-10) cc_final: 0.6787 (m-10) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1535 time to fit residues: 70.1215 Evaluate side-chains 211 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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: 2.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN A 405 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.188531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.149276 restraints weight = 29055.227| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.74 r_work: 0.3272 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25424 Z= 0.150 Angle : 0.587 10.969 34662 Z= 0.300 Chirality : 0.045 0.223 4009 Planarity : 0.004 0.077 4424 Dihedral : 7.300 106.391 3951 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.88 % Allowed : 6.26 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.03 (0.14), residues: 3081 helix: 1.09 (0.20), residues: 668 sheet: 0.01 (0.20), residues: 657 loop : -1.76 (0.13), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 646 TYR 0.013 0.001 TYR C 351 PHE 0.026 0.001 PHE C 168 TRP 0.011 0.001 TRP C 886 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00351 (25354) covalent geometry : angle 0.56820 (34493) SS BOND : bond 0.00350 ( 41) SS BOND : angle 1.85451 ( 82) hydrogen bonds : bond 0.05427 ( 882) hydrogen bonds : angle 5.31544 ( 2466) link_NAG-ASN : bond 0.00519 ( 29) link_NAG-ASN : angle 2.41705 ( 87) *********************** 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 268 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.7908 (m-80) cc_final: 0.7519 (m-80) REVERT: C 537 LYS cc_start: 0.6973 (mtpp) cc_final: 0.6605 (mttt) REVERT: C 544 ASN cc_start: 0.8942 (m-40) cc_final: 0.8603 (m-40) REVERT: B 420 ASP cc_start: 0.7788 (m-30) cc_final: 0.7498 (m-30) REVERT: B 646 ARG cc_start: 0.7878 (mtp180) cc_final: 0.7479 (ttt90) REVERT: B 1138 TYR cc_start: 0.7517 (t80) cc_final: 0.7061 (t80) REVERT: A 287 ASP cc_start: 0.7119 (m-30) cc_final: 0.6740 (m-30) REVERT: A 811 LYS cc_start: 0.7032 (mmtm) cc_final: 0.6201 (tttp) REVERT: A 904 TYR cc_start: 0.7520 (m-10) cc_final: 0.7208 (m-10) outliers start: 24 outliers final: 18 residues processed: 258 average time/residue: 0.1645 time to fit residues: 68.2049 Evaluate side-chains 233 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 881 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 49 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 310 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 280 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN C 519 HIS C1135 ASN B 314 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 960 ASN A1083 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.182144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.142151 restraints weight = 29215.908| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.68 r_work: 0.3276 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 25424 Z= 0.231 Angle : 0.637 8.667 34662 Z= 0.327 Chirality : 0.047 0.265 4009 Planarity : 0.004 0.058 4424 Dihedral : 6.889 96.467 3951 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.84 % Allowed : 9.17 % Favored : 88.99 % 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: -1.03 (0.14), residues: 3081 helix: 1.17 (0.20), residues: 682 sheet: -0.26 (0.21), residues: 600 loop : -1.64 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 646 TYR 0.016 0.002 TYR C 266 PHE 0.029 0.002 PHE A 392 TRP 0.012 0.002 TRP A 436 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00568 (25354) covalent geometry : angle 0.61827 (34493) SS BOND : bond 0.00807 ( 41) SS BOND : angle 2.18924 ( 82) hydrogen bonds : bond 0.06401 ( 882) hydrogen bonds : angle 5.18839 ( 2466) link_NAG-ASN : bond 0.00589 ( 29) link_NAG-ASN : angle 2.36541 ( 87) *********************** 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 284 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 234 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 332 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7078 (mm) REVERT: C 340 GLU cc_start: 0.8100 (mp0) cc_final: 0.7833 (mp0) REVERT: C 430 THR cc_start: 0.7760 (p) cc_final: 0.7458 (m) REVERT: C 466 ARG cc_start: 0.7490 (ttm170) cc_final: 0.7288 (ttm170) REVERT: C 537 LYS cc_start: 0.7436 (mtpp) cc_final: 0.7144 (tppt) REVERT: C 544 ASN cc_start: 0.9047 (m-40) cc_final: 0.8816 (m-40) REVERT: B 422 ASN cc_start: 0.7759 (t0) cc_final: 0.7547 (m110) REVERT: B 646 ARG cc_start: 0.7968 (mtp180) cc_final: 0.7478 (ttt90) REVERT: B 977 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8192 (mp) REVERT: B 1107 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7203 (mmm160) REVERT: A 287 ASP cc_start: 0.7379 (m-30) cc_final: 0.7005 (m-30) REVERT: A 339 HIS cc_start: 0.8345 (t70) cc_final: 0.8019 (t70) REVERT: A 588 THR cc_start: 0.8889 (m) cc_final: 0.8675 (p) REVERT: A 811 LYS cc_start: 0.7129 (mmtm) cc_final: 0.6263 (tttp) REVERT: A 904 TYR cc_start: 0.7774 (m-10) cc_final: 0.7231 (m-10) outliers start: 50 outliers final: 38 residues processed: 268 average time/residue: 0.1698 time to fit residues: 73.4412 Evaluate side-chains 255 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 294 optimal weight: 0.0980 chunk 254 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 278 optimal weight: 0.0000 chunk 264 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN A1083 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.186355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.147274 restraints weight = 28933.302| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.63 r_work: 0.3156 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25424 Z= 0.107 Angle : 0.529 9.585 34662 Z= 0.270 Chirality : 0.043 0.271 4009 Planarity : 0.004 0.058 4424 Dihedral : 6.036 81.099 3951 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.18 % Allowed : 11.20 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.65 (0.15), residues: 3081 helix: 1.87 (0.20), residues: 668 sheet: -0.23 (0.20), residues: 682 loop : -1.52 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.017 0.001 TYR A1138 PHE 0.023 0.001 PHE A 392 TRP 0.009 0.001 TRP C 886 HIS 0.004 0.000 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00242 (25354) covalent geometry : angle 0.51195 (34493) SS BOND : bond 0.00299 ( 41) SS BOND : angle 1.69570 ( 82) hydrogen bonds : bond 0.04753 ( 882) hydrogen bonds : angle 4.76091 ( 2466) link_NAG-ASN : bond 0.00489 ( 29) link_NAG-ASN : angle 2.17463 ( 87) *********************** 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 261 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8059 (m-80) cc_final: 0.7617 (m-80) REVERT: C 332 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7203 (mm) REVERT: C 340 GLU cc_start: 0.8128 (mp0) cc_final: 0.7828 (mp0) REVERT: C 396 TYR cc_start: 0.8088 (m-80) cc_final: 0.7676 (m-80) REVERT: C 430 THR cc_start: 0.7715 (p) cc_final: 0.7485 (m) REVERT: C 537 LYS cc_start: 0.7271 (mtpp) cc_final: 0.6988 (tppt) REVERT: C 675 GLN cc_start: 0.7034 (pp30) cc_final: 0.6530 (pp30) REVERT: C 902 MET cc_start: 0.8982 (tpt) cc_final: 0.8738 (mmm) REVERT: C 1073 LYS cc_start: 0.7815 (ptmm) cc_final: 0.7103 (mtpt) REVERT: B 420 ASP cc_start: 0.7873 (m-30) cc_final: 0.7655 (m-30) REVERT: B 422 ASN cc_start: 0.7710 (t0) cc_final: 0.7292 (m110) REVERT: B 646 ARG cc_start: 0.7943 (mtp180) cc_final: 0.7378 (ttt90) REVERT: A 201 PHE cc_start: 0.5830 (m-80) cc_final: 0.5582 (m-80) REVERT: A 224 GLU cc_start: 0.6541 (mp0) cc_final: 0.6099 (mp0) REVERT: A 287 ASP cc_start: 0.7228 (m-30) cc_final: 0.6826 (m-30) REVERT: A 339 HIS cc_start: 0.8395 (t70) cc_final: 0.8079 (t70) REVERT: A 371 PHE cc_start: 0.8141 (m-10) cc_final: 0.7650 (m-80) REVERT: A 811 LYS cc_start: 0.7254 (mmtm) cc_final: 0.6361 (tttp) REVERT: A 904 TYR cc_start: 0.7826 (m-10) cc_final: 0.7413 (m-10) outliers start: 32 outliers final: 22 residues processed: 254 average time/residue: 0.1668 time to fit residues: 69.0305 Evaluate side-chains 241 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 1 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 301 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 307 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.172231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131932 restraints weight = 29774.859| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.17 r_work: 0.3123 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25424 Z= 0.200 Angle : 0.602 9.640 34662 Z= 0.308 Chirality : 0.046 0.260 4009 Planarity : 0.004 0.058 4424 Dihedral : 6.034 70.365 3951 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.25 % Allowed : 12.08 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.80 (0.15), residues: 3081 helix: 1.59 (0.20), residues: 684 sheet: -0.35 (0.20), residues: 650 loop : -1.53 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.015 0.001 TYR B 421 PHE 0.031 0.002 PHE A 392 TRP 0.011 0.001 TRP C 886 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00491 (25354) covalent geometry : angle 0.58231 (34493) SS BOND : bond 0.00436 ( 41) SS BOND : angle 2.13488 ( 82) hydrogen bonds : bond 0.05894 ( 882) hydrogen bonds : angle 4.91810 ( 2466) link_NAG-ASN : bond 0.00430 ( 29) link_NAG-ASN : angle 2.34762 ( 87) *********************** 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 285 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 224 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: C 332 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7283 (mm) REVERT: C 340 GLU cc_start: 0.8129 (mp0) cc_final: 0.7770 (mp0) REVERT: C 396 TYR cc_start: 0.8103 (m-80) cc_final: 0.7752 (m-80) REVERT: C 430 THR cc_start: 0.7789 (p) cc_final: 0.7576 (m) REVERT: C 537 LYS cc_start: 0.7651 (mtpp) cc_final: 0.7394 (tppt) REVERT: C 564 GLN cc_start: 0.8318 (tp40) cc_final: 0.7843 (tp40) REVERT: C 675 GLN cc_start: 0.7327 (pp30) cc_final: 0.6600 (pp30) REVERT: B 383 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8234 (p) REVERT: B 422 ASN cc_start: 0.7772 (t0) cc_final: 0.7342 (m110) REVERT: B 646 ARG cc_start: 0.7819 (mtp180) cc_final: 0.7310 (ttt90) REVERT: B 834 ILE cc_start: 0.5371 (OUTLIER) cc_final: 0.5142 (tp) REVERT: B 1107 ARG cc_start: 0.7844 (mtt180) cc_final: 0.7151 (mmm160) REVERT: A 224 GLU cc_start: 0.6625 (mp0) cc_final: 0.6163 (mp0) REVERT: A 287 ASP cc_start: 0.7228 (m-30) cc_final: 0.6867 (m-30) REVERT: A 339 HIS cc_start: 0.8327 (t70) cc_final: 0.8088 (t70) REVERT: A 588 THR cc_start: 0.8829 (m) cc_final: 0.8622 (p) REVERT: A 620 VAL cc_start: 0.7101 (OUTLIER) cc_final: 0.6887 (t) REVERT: A 675 GLN cc_start: 0.5687 (mm-40) cc_final: 0.5456 (tt0) REVERT: A 811 LYS cc_start: 0.7369 (mmtm) cc_final: 0.6475 (tttm) REVERT: A 904 TYR cc_start: 0.7584 (m-10) cc_final: 0.7009 (m-10) outliers start: 61 outliers final: 41 residues processed: 267 average time/residue: 0.1694 time to fit residues: 73.1439 Evaluate side-chains 261 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 204 optimal weight: 0.6980 chunk 40 optimal weight: 0.0000 chunk 57 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 270 optimal weight: 0.9990 chunk 263 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 221 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 224 optimal weight: 0.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.175675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.135720 restraints weight = 29641.179| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.88 r_work: 0.3277 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25424 Z= 0.112 Angle : 0.535 9.266 34662 Z= 0.272 Chirality : 0.044 0.263 4009 Planarity : 0.004 0.050 4424 Dihedral : 5.626 58.387 3951 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.80 % Allowed : 13.11 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.58 (0.15), residues: 3081 helix: 1.95 (0.20), residues: 683 sheet: -0.15 (0.21), residues: 632 loop : -1.50 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.017 0.001 TYR A1138 PHE 0.025 0.001 PHE A 392 TRP 0.008 0.001 TRP A 886 HIS 0.003 0.000 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00256 (25354) covalent geometry : angle 0.51729 (34493) SS BOND : bond 0.00320 ( 41) SS BOND : angle 1.77744 ( 82) hydrogen bonds : bond 0.04826 ( 882) hydrogen bonds : angle 4.67983 ( 2466) link_NAG-ASN : bond 0.00428 ( 29) link_NAG-ASN : angle 2.22317 ( 87) *********************** 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 277 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: C 200 TYR cc_start: 0.7984 (m-80) cc_final: 0.7709 (m-80) REVERT: C 332 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7148 (mm) REVERT: C 340 GLU cc_start: 0.8104 (mp0) cc_final: 0.7756 (mp0) REVERT: C 396 TYR cc_start: 0.8067 (m-80) cc_final: 0.7648 (m-80) REVERT: C 451 TYR cc_start: 0.7063 (m-10) cc_final: 0.6846 (m-10) REVERT: C 537 LYS cc_start: 0.7516 (mtpp) cc_final: 0.7227 (tppt) REVERT: C 564 GLN cc_start: 0.8256 (tp40) cc_final: 0.7785 (tp40) REVERT: C 674 TYR cc_start: 0.8633 (t80) cc_final: 0.8196 (t80) REVERT: C 675 GLN cc_start: 0.7234 (pp30) cc_final: 0.6583 (pp30) REVERT: C 1073 LYS cc_start: 0.7720 (ptmm) cc_final: 0.7101 (mtpt) REVERT: B 125 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7623 (m-40) REVERT: B 422 ASN cc_start: 0.7752 (t0) cc_final: 0.7489 (m-40) REVERT: B 646 ARG cc_start: 0.7761 (mtp180) cc_final: 0.7253 (ttt90) REVERT: B 936 ASP cc_start: 0.7800 (t0) cc_final: 0.7474 (t0) REVERT: B 1107 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7151 (mmm160) REVERT: A 224 GLU cc_start: 0.6626 (mp0) cc_final: 0.6172 (mp0) REVERT: A 287 ASP cc_start: 0.7227 (m-30) cc_final: 0.6863 (m-30) REVERT: A 620 VAL cc_start: 0.7051 (OUTLIER) cc_final: 0.6848 (t) REVERT: A 675 GLN cc_start: 0.5738 (mm-40) cc_final: 0.5527 (tt0) REVERT: A 811 LYS cc_start: 0.7388 (mmtm) cc_final: 0.6577 (tttt) REVERT: A 904 TYR cc_start: 0.7535 (m-10) cc_final: 0.7090 (m-10) outliers start: 49 outliers final: 33 residues processed: 264 average time/residue: 0.1669 time to fit residues: 71.7492 Evaluate side-chains 253 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 874 THR 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 43 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 259 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 1 optimal weight: 0.4980 chunk 211 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN C 544 ASN B 125 ASN B 422 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS A1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.170596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.128499 restraints weight = 29811.049| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.38 r_work: 0.3086 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25424 Z= 0.191 Angle : 0.591 8.124 34662 Z= 0.302 Chirality : 0.046 0.251 4009 Planarity : 0.004 0.045 4424 Dihedral : 5.677 57.919 3951 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.54 % Allowed : 12.82 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.76 (0.20), residues: 685 sheet: -0.32 (0.20), residues: 652 loop : -1.50 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.015 0.001 TYR B 421 PHE 0.028 0.002 PHE A 392 TRP 0.010 0.001 TRP B 104 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00472 (25354) covalent geometry : angle 0.57142 (34493) SS BOND : bond 0.00423 ( 41) SS BOND : angle 2.04348 ( 82) hydrogen bonds : bond 0.05676 ( 882) hydrogen bonds : angle 4.81143 ( 2466) link_NAG-ASN : bond 0.00391 ( 29) link_NAG-ASN : angle 2.35361 ( 87) *********************** 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 293 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 224 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: C 396 TYR cc_start: 0.8045 (m-80) cc_final: 0.7691 (m-80) REVERT: C 537 LYS cc_start: 0.7699 (mtpp) cc_final: 0.7377 (tppt) REVERT: C 564 GLN cc_start: 0.8335 (tp40) cc_final: 0.7843 (tp40) REVERT: C 675 GLN cc_start: 0.7222 (pp30) cc_final: 0.6578 (pp30) REVERT: C 1073 LYS cc_start: 0.7693 (ptmm) cc_final: 0.7075 (mtpt) REVERT: B 383 SER cc_start: 0.8806 (OUTLIER) cc_final: 0.8272 (p) REVERT: B 422 ASN cc_start: 0.7979 (OUTLIER) cc_final: 0.7546 (m-40) REVERT: B 646 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7218 (ttt90) REVERT: B 834 ILE cc_start: 0.5414 (OUTLIER) cc_final: 0.4979 (tp) REVERT: B 1107 ARG cc_start: 0.7905 (mtt180) cc_final: 0.7082 (mmm160) REVERT: A 224 GLU cc_start: 0.6618 (mp0) cc_final: 0.6132 (mp0) REVERT: A 242 LEU cc_start: 0.3224 (OUTLIER) cc_final: 0.3004 (tt) REVERT: A 287 ASP cc_start: 0.7227 (m-30) cc_final: 0.6851 (m-30) REVERT: A 675 GLN cc_start: 0.5603 (mm-40) cc_final: 0.5318 (tt0) REVERT: A 811 LYS cc_start: 0.7412 (mmtm) cc_final: 0.6449 (tttm) REVERT: A 904 TYR cc_start: 0.7640 (m-10) cc_final: 0.7082 (m-10) outliers start: 69 outliers final: 47 residues processed: 273 average time/residue: 0.1684 time to fit residues: 74.5731 Evaluate side-chains 261 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 210 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 121 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 257 optimal weight: 0.0870 chunk 296 optimal weight: 0.8980 chunk 290 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 235 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A1083 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.172078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130286 restraints weight = 29722.346| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.22 r_work: 0.3136 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25424 Z= 0.138 Angle : 0.560 10.473 34662 Z= 0.285 Chirality : 0.044 0.252 4009 Planarity : 0.004 0.042 4424 Dihedral : 5.508 58.054 3951 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.03 % Allowed : 13.63 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.93 (0.20), residues: 683 sheet: -0.31 (0.20), residues: 652 loop : -1.45 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.021 0.001 TYR B 421 PHE 0.022 0.001 PHE A 392 TRP 0.009 0.001 TRP C 886 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00330 (25354) covalent geometry : angle 0.54194 (34493) SS BOND : bond 0.00349 ( 41) SS BOND : angle 1.87693 ( 82) hydrogen bonds : bond 0.05145 ( 882) hydrogen bonds : angle 4.69903 ( 2466) link_NAG-ASN : bond 0.00385 ( 29) link_NAG-ASN : angle 2.27916 ( 87) *********************** 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 270 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 215 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 396 TYR cc_start: 0.8040 (m-80) cc_final: 0.7624 (m-80) REVERT: C 537 LYS cc_start: 0.7721 (mtpp) cc_final: 0.7410 (tppt) REVERT: C 564 GLN cc_start: 0.8208 (tp40) cc_final: 0.7733 (tp40) REVERT: C 675 GLN cc_start: 0.7144 (pp30) cc_final: 0.6550 (pp30) REVERT: C 1073 LYS cc_start: 0.7600 (ptmm) cc_final: 0.7027 (mtpt) REVERT: B 200 TYR cc_start: 0.7898 (m-10) cc_final: 0.7516 (m-80) REVERT: B 383 SER cc_start: 0.8795 (OUTLIER) cc_final: 0.8283 (p) REVERT: B 422 ASN cc_start: 0.7858 (t0) cc_final: 0.7485 (m110) REVERT: B 646 ARG cc_start: 0.7808 (mtp180) cc_final: 0.7204 (ttt90) REVERT: B 1107 ARG cc_start: 0.7904 (mtt180) cc_final: 0.7084 (mmm160) REVERT: A 224 GLU cc_start: 0.6595 (mp0) cc_final: 0.6126 (mp0) REVERT: A 242 LEU cc_start: 0.3260 (OUTLIER) cc_final: 0.3032 (tt) REVERT: A 287 ASP cc_start: 0.7197 (m-30) cc_final: 0.6827 (m-30) REVERT: A 675 GLN cc_start: 0.5647 (mm-40) cc_final: 0.5368 (tt0) REVERT: A 811 LYS cc_start: 0.7397 (mmtm) cc_final: 0.6512 (tttm) REVERT: A 904 TYR cc_start: 0.7650 (m-10) cc_final: 0.7154 (m-10) outliers start: 55 outliers final: 46 residues processed: 253 average time/residue: 0.1673 time to fit residues: 69.0361 Evaluate side-chains 260 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 THR 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 190 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 235 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 294 optimal weight: 0.6980 chunk 137 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.169427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.127192 restraints weight = 29746.702| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.29 r_work: 0.3054 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25424 Z= 0.164 Angle : 0.572 7.970 34662 Z= 0.291 Chirality : 0.045 0.242 4009 Planarity : 0.004 0.043 4424 Dihedral : 5.514 57.841 3951 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.36 % Allowed : 13.55 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.88 (0.20), residues: 683 sheet: -0.32 (0.21), residues: 653 loop : -1.48 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.019 0.001 TYR A1138 PHE 0.022 0.001 PHE A 392 TRP 0.009 0.001 TRP B 104 HIS 0.011 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00401 (25354) covalent geometry : angle 0.55368 (34493) SS BOND : bond 0.00392 ( 41) SS BOND : angle 1.96505 ( 82) hydrogen bonds : bond 0.05341 ( 882) hydrogen bonds : angle 4.74104 ( 2466) link_NAG-ASN : bond 0.00364 ( 29) link_NAG-ASN : angle 2.28278 ( 87) *********************** 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 278 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 214 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 396 TYR cc_start: 0.8089 (m-80) cc_final: 0.7640 (m-80) REVERT: C 506 GLN cc_start: 0.8404 (mp10) cc_final: 0.7937 (mp10) REVERT: C 537 LYS cc_start: 0.7738 (mtpp) cc_final: 0.7388 (tppt) REVERT: C 564 GLN cc_start: 0.8200 (tp40) cc_final: 0.7703 (tp40) REVERT: C 675 GLN cc_start: 0.7038 (pp30) cc_final: 0.6447 (pp30) REVERT: C 935 GLN cc_start: 0.7313 (tp40) cc_final: 0.6916 (tt0) REVERT: C 1073 LYS cc_start: 0.7576 (ptmm) cc_final: 0.6986 (mtpt) REVERT: B 422 ASN cc_start: 0.7811 (t0) cc_final: 0.7328 (m-40) REVERT: B 646 ARG cc_start: 0.7859 (mtp180) cc_final: 0.7214 (ttt90) REVERT: B 834 ILE cc_start: 0.5369 (OUTLIER) cc_final: 0.4971 (tp) REVERT: B 1107 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7038 (mmm160) REVERT: A 224 GLU cc_start: 0.6547 (mp0) cc_final: 0.6093 (mp0) REVERT: A 242 LEU cc_start: 0.3397 (OUTLIER) cc_final: 0.3168 (tt) REVERT: A 287 ASP cc_start: 0.7164 (m-30) cc_final: 0.6783 (m-30) REVERT: A 675 GLN cc_start: 0.5573 (mm-40) cc_final: 0.5232 (tt0) REVERT: A 811 LYS cc_start: 0.7399 (mmtm) cc_final: 0.6482 (tttm) REVERT: A 904 TYR cc_start: 0.7676 (m-10) cc_final: 0.7200 (m-10) outliers start: 64 outliers final: 57 residues processed: 258 average time/residue: 0.1648 time to fit residues: 69.4935 Evaluate side-chains 269 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 210 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 24 optimal weight: 6.9990 chunk 147 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 290 optimal weight: 0.9990 chunk 226 optimal weight: 30.0000 chunk 300 optimal weight: 0.7980 chunk 294 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.173760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131870 restraints weight = 29717.681| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 3.06 r_work: 0.3179 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25424 Z= 0.111 Angle : 0.536 9.006 34662 Z= 0.273 Chirality : 0.044 0.245 4009 Planarity : 0.004 0.041 4424 Dihedral : 5.255 57.737 3951 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.84 % Allowed : 14.11 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.49 (0.15), residues: 3081 helix: 2.11 (0.20), residues: 684 sheet: -0.18 (0.20), residues: 646 loop : -1.45 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.018 0.001 TYR A1138 PHE 0.016 0.001 PHE C 464 TRP 0.009 0.001 TRP A 886 HIS 0.003 0.000 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00256 (25354) covalent geometry : angle 0.51945 (34493) SS BOND : bond 0.00306 ( 41) SS BOND : angle 1.71814 ( 82) hydrogen bonds : bond 0.04612 ( 882) hydrogen bonds : angle 4.58265 ( 2466) link_NAG-ASN : bond 0.00400 ( 29) link_NAG-ASN : angle 2.15460 ( 87) ********************** 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 278 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: C 100 ILE cc_start: 0.8723 (mm) cc_final: 0.8509 (mt) REVERT: C 200 TYR cc_start: 0.8002 (m-80) cc_final: 0.7752 (m-80) REVERT: C 396 TYR cc_start: 0.8098 (m-80) cc_final: 0.7659 (m-80) REVERT: C 441 LEU cc_start: 0.7888 (mp) cc_final: 0.7686 (mt) REVERT: C 506 GLN cc_start: 0.8460 (mp10) cc_final: 0.8023 (mp10) REVERT: C 537 LYS cc_start: 0.7704 (mtpp) cc_final: 0.7398 (tppt) REVERT: C 564 GLN cc_start: 0.8244 (tp40) cc_final: 0.7777 (tp40) REVERT: C 675 GLN cc_start: 0.7116 (pp30) cc_final: 0.6518 (pp30) REVERT: C 902 MET cc_start: 0.8974 (tpt) cc_final: 0.8554 (tpt) REVERT: C 1073 LYS cc_start: 0.7662 (ptmm) cc_final: 0.7129 (mtpt) REVERT: B 383 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8264 (p) REVERT: B 422 ASN cc_start: 0.7882 (t0) cc_final: 0.7530 (m-40) REVERT: B 646 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7167 (ttt90) REVERT: B 697 MET cc_start: 0.7582 (mmt) cc_final: 0.7312 (mmt) REVERT: B 834 ILE cc_start: 0.5420 (OUTLIER) cc_final: 0.5019 (tp) REVERT: B 1107 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7058 (mmm160) REVERT: A 224 GLU cc_start: 0.6572 (mp0) cc_final: 0.6130 (mp0) REVERT: A 287 ASP cc_start: 0.7188 (m-30) cc_final: 0.6828 (m-30) REVERT: A 675 GLN cc_start: 0.5670 (mm-40) cc_final: 0.5382 (tt0) REVERT: A 811 LYS cc_start: 0.7485 (mmtm) cc_final: 0.6668 (tttm) REVERT: A 904 TYR cc_start: 0.7563 (m-10) cc_final: 0.7064 (m-10) outliers start: 50 outliers final: 42 residues processed: 265 average time/residue: 0.1650 time to fit residues: 71.0513 Evaluate side-chains 261 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 874 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 208 optimal weight: 20.0000 chunk 163 optimal weight: 4.9990 chunk 292 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 204 optimal weight: 0.8980 chunk 306 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 422 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.180027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140905 restraints weight = 29176.924| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.70 r_work: 0.3173 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25424 Z= 0.213 Angle : 0.618 12.555 34662 Z= 0.316 Chirality : 0.047 0.229 4009 Planarity : 0.004 0.048 4424 Dihedral : 5.592 57.895 3951 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.10 % Allowed : 14.00 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.66 (0.15), residues: 3081 helix: 1.76 (0.20), residues: 687 sheet: -0.26 (0.20), residues: 663 loop : -1.49 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.019 0.001 TYR A1138 PHE 0.024 0.002 PHE A 392 TRP 0.011 0.001 TRP B 104 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00527 (25354) covalent geometry : angle 0.60008 (34493) SS BOND : bond 0.00449 ( 41) SS BOND : angle 2.12389 ( 82) hydrogen bonds : bond 0.05878 ( 882) hydrogen bonds : angle 4.85460 ( 2466) link_NAG-ASN : bond 0.00365 ( 29) link_NAG-ASN : angle 2.32035 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6087.74 seconds wall clock time: 105 minutes 29.93 seconds (6329.93 seconds total)