Starting phenix.real_space_refine on Sat Jun 21 13:12:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0x_42873/06_2025/8v0x_42873.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0x_42873/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8v0x_42873/06_2025/8v0x_42873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0x_42873/06_2025/8v0x_42873.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0x_42873/06_2025/8v0x_42873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0x_42873/06_2025/8v0x_42873.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.22, per 1000 atoms: 0.57 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: 5.67 Conformation dependent library (CDL) restraints added in 3.2 seconds 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5862 Finding SS restraints... Secondary structure from input PDB file: 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: 3.96 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: 12.18 Time building geometry restraints manager: 6.90 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 1147 or resid 1301 through 1309)) selection = (chain 'B' and (resid 24 through 1147 or resid 1301 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: 2.150 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: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 58.950 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (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 TRP 0.013 0.001 TRP C 886 HIS 0.013 0.001 HIS C 519 PHE 0.047 0.002 PHE C 168 TYR 0.028 0.001 TYR B 170 ARG 0.013 0.001 ARG B 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 29) link_NAG-ASN : angle 2.76216 ( 87) hydrogen bonds : bond 0.21040 ( 882) hydrogen bonds : angle 7.43664 ( 2466) SS BOND : bond 0.00538 ( 41) SS BOND : angle 1.75621 ( 82) covalent geometry : bond 0.00422 (25354) covalent geometry : angle 0.79083 (34493) *********************** 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 : 2.731 Fit side-chains revert: symmetry clash 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: 0.6463 (m-30) 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: 0.3408 time to fit residues: 156.5561 Evaluate side-chains 212 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.0170 chunk 236 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 80 optimal weight: 0.0870 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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** C 519 HIS B 544 ASN B 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.182277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.142564 restraints weight = 29565.905| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.67 r_work: 0.3369 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25424 Z= 0.114 Angle : 0.545 10.267 34662 Z= 0.281 Chirality : 0.044 0.227 4009 Planarity : 0.004 0.076 4424 Dihedral : 6.917 106.990 3951 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.70 % Allowed : 5.89 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3081 helix: 1.27 (0.20), residues: 671 sheet: 0.08 (0.20), residues: 657 loop : -1.73 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.006 0.001 HIS C 519 PHE 0.026 0.001 PHE C 168 TYR 0.014 0.001 TYR A 265 ARG 0.004 0.000 ARG C 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 29) link_NAG-ASN : angle 2.24532 ( 87) hydrogen bonds : bond 0.04901 ( 882) hydrogen bonds : angle 5.24772 ( 2466) SS BOND : bond 0.00368 ( 41) SS BOND : angle 1.63258 ( 82) covalent geometry : bond 0.00242 (25354) covalent geometry : angle 0.52864 (34493) *********************** 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 275 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 256 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 493 GLN cc_start: 0.7610 (tt0) cc_final: 0.7188 (tt0) REVERT: C 537 LYS cc_start: 0.6929 (mtpp) cc_final: 0.6555 (mttt) REVERT: C 544 ASN cc_start: 0.8890 (m-40) cc_final: 0.8581 (m-40) REVERT: B 303 LEU cc_start: 0.8710 (mt) cc_final: 0.8377 (mt) REVERT: B 420 ASP cc_start: 0.7855 (m-30) cc_final: 0.7602 (m-30) REVERT: B 646 ARG cc_start: 0.7885 (mtp180) cc_final: 0.7490 (ttt90) REVERT: B 1138 TYR cc_start: 0.7472 (t80) cc_final: 0.7018 (t80) REVERT: A 224 GLU cc_start: 0.6520 (mp0) cc_final: 0.6252 (mp0) REVERT: A 287 ASP cc_start: 0.7099 (m-30) cc_final: 0.6724 (m-30) REVERT: A 811 LYS cc_start: 0.6939 (mmtm) cc_final: 0.6161 (tttp) REVERT: A 904 TYR cc_start: 0.7506 (m-10) cc_final: 0.7202 (m-10) outliers start: 19 outliers final: 14 residues processed: 265 average time/residue: 0.3450 time to fit residues: 150.4090 Evaluate side-chains 232 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 2.894 ------------------------------------------------------------------------------- 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 547 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain B residue 51 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 934 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 828 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 161 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 158 optimal weight: 0.7980 chunk 290 optimal weight: 0.9980 chunk 287 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 297 optimal weight: 0.9980 chunk 241 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 188 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A 960 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.189069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.149972 restraints weight = 28738.953| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.59 r_work: 0.3198 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1291 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= 0.121 Angle : 0.532 8.774 34662 Z= 0.272 Chirality : 0.044 0.290 4009 Planarity : 0.004 0.056 4424 Dihedral : 6.346 96.948 3951 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.22 % Allowed : 8.66 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3081 helix: 1.69 (0.20), residues: 674 sheet: 0.04 (0.20), residues: 651 loop : -1.57 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS B 339 PHE 0.028 0.001 PHE A 541 TYR 0.012 0.001 TYR A 489 ARG 0.006 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00502 ( 29) link_NAG-ASN : angle 1.99853 ( 87) hydrogen bonds : bond 0.04854 ( 882) hydrogen bonds : angle 4.86149 ( 2466) SS BOND : bond 0.00287 ( 41) SS BOND : angle 1.69621 ( 82) covalent geometry : bond 0.00284 (25354) covalent geometry : angle 0.51746 (34493) *********************** 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 266 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 3.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.7892 (m-80) cc_final: 0.7569 (m-80) REVERT: C 430 THR cc_start: 0.7829 (p) cc_final: 0.7594 (m) REVERT: C 537 LYS cc_start: 0.7003 (mtpp) cc_final: 0.6543 (mttt) REVERT: C 544 ASN cc_start: 0.8970 (m-40) cc_final: 0.8617 (m-40) REVERT: C 576 VAL cc_start: 0.7522 (p) cc_final: 0.7294 (t) REVERT: B 224 GLU cc_start: 0.8193 (mp0) cc_final: 0.7758 (mp0) REVERT: B 420 ASP cc_start: 0.7978 (m-30) cc_final: 0.7555 (m-30) REVERT: B 646 ARG cc_start: 0.7970 (mtp180) cc_final: 0.7433 (ttt90) REVERT: A 43 PHE cc_start: 0.7388 (t80) cc_final: 0.7175 (t80) REVERT: A 53 ASP cc_start: 0.7186 (t0) cc_final: 0.6984 (t0) REVERT: A 224 GLU cc_start: 0.6526 (mp0) cc_final: 0.6248 (mp0) REVERT: A 287 ASP cc_start: 0.7187 (m-30) cc_final: 0.6808 (m-30) REVERT: A 811 LYS cc_start: 0.7032 (mmtm) cc_final: 0.6048 (tttp) REVERT: A 904 TYR cc_start: 0.7699 (m-10) cc_final: 0.7443 (m-10) outliers start: 33 outliers final: 23 residues processed: 255 average time/residue: 0.3514 time to fit residues: 145.5088 Evaluate side-chains 240 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 2.782 ------------------------------------------------------------------------------- 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 455 LEU 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 951 VAL Chi-restraints excluded: chain B residue 108 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 525 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 214 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 212 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1135 ASN B 314 GLN B 506 GLN B 613 GLN A 414 GLN A1083 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.181223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141520 restraints weight = 29375.673| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.79 r_work: 0.3203 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 25424 Z= 0.242 Angle : 0.651 9.465 34662 Z= 0.335 Chirality : 0.048 0.271 4009 Planarity : 0.004 0.051 4424 Dihedral : 6.405 82.021 3951 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.17 % Allowed : 9.61 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3081 helix: 1.32 (0.20), residues: 683 sheet: -0.36 (0.20), residues: 668 loop : -1.59 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 436 HIS 0.007 0.001 HIS B1064 PHE 0.036 0.002 PHE A 92 TYR 0.019 0.002 TYR A 91 ARG 0.004 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 29) link_NAG-ASN : angle 2.32631 ( 87) hydrogen bonds : bond 0.06480 ( 882) hydrogen bonds : angle 5.10453 ( 2466) SS BOND : bond 0.00580 ( 41) SS BOND : angle 2.25413 ( 82) covalent geometry : bond 0.00599 (25354) covalent geometry : angle 0.63206 (34493) *********************** 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 304 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 245 time to evaluate : 2.580 Fit side-chains revert: symmetry clash REVERT: C 332 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7155 (mm) REVERT: C 340 GLU cc_start: 0.8135 (mp0) cc_final: 0.7852 (mp0) REVERT: C 396 TYR cc_start: 0.8103 (m-80) cc_final: 0.7744 (m-80) REVERT: C 430 THR cc_start: 0.7869 (p) cc_final: 0.7660 (m) REVERT: C 532 ASN cc_start: 0.7605 (t0) cc_final: 0.7368 (t0) REVERT: C 537 LYS cc_start: 0.7547 (mtpp) cc_final: 0.7267 (tppt) REVERT: C 544 ASN cc_start: 0.9026 (m-40) cc_final: 0.8767 (m-40) REVERT: C 675 GLN cc_start: 0.7231 (pp30) cc_final: 0.6697 (pp30) REVERT: B 106 PHE cc_start: 0.7721 (m-80) cc_final: 0.7520 (m-80) REVERT: B 224 GLU cc_start: 0.8358 (mp0) cc_final: 0.7878 (mp0) REVERT: B 646 ARG cc_start: 0.7850 (mtp180) cc_final: 0.7374 (ttt90) REVERT: B 936 ASP cc_start: 0.7773 (t0) cc_final: 0.7401 (t0) REVERT: B 977 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8115 (mp) REVERT: B 1107 ARG cc_start: 0.7829 (mtt180) cc_final: 0.7168 (mmm160) REVERT: A 53 ASP cc_start: 0.7308 (t0) cc_final: 0.6959 (t0) REVERT: A 287 ASP cc_start: 0.7148 (m-30) cc_final: 0.6764 (m-30) REVERT: A 588 THR cc_start: 0.8824 (m) cc_final: 0.8621 (p) REVERT: A 811 LYS cc_start: 0.7295 (mmtm) cc_final: 0.6405 (tttp) REVERT: A 904 TYR cc_start: 0.7524 (m-10) cc_final: 0.6935 (m-10) outliers start: 59 outliers final: 44 residues processed: 287 average time/residue: 0.3384 time to fit residues: 158.2722 Evaluate side-chains 264 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 2.496 ------------------------------------------------------------------------------- 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 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 422 ASN 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 878 LEU 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 51 THR Chi-restraints excluded: chain B residue 87 ASN 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 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 745 ASP 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 40 ASP Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 547 THR 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 1027 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 294 optimal weight: 0.0770 chunk 240 optimal weight: 0.9980 chunk 251 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 125 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN A1083 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.183862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.144697 restraints weight = 29104.095| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.60 r_work: 0.3306 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25424 Z= 0.111 Angle : 0.551 12.862 34662 Z= 0.277 Chirality : 0.044 0.266 4009 Planarity : 0.004 0.052 4424 Dihedral : 5.867 69.797 3951 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.47 % Allowed : 12.08 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3081 helix: 1.89 (0.20), residues: 682 sheet: -0.09 (0.20), residues: 629 loop : -1.50 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 886 HIS 0.003 0.000 HIS B1083 PHE 0.023 0.001 PHE A 392 TYR 0.017 0.001 TYR A1138 ARG 0.004 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 29) link_NAG-ASN : angle 2.14950 ( 87) hydrogen bonds : bond 0.04897 ( 882) hydrogen bonds : angle 4.79493 ( 2466) SS BOND : bond 0.00289 ( 41) SS BOND : angle 1.78270 ( 82) covalent geometry : bond 0.00249 (25354) covalent geometry : angle 0.53516 (34493) *********************** 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 269 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 2.641 Fit side-chains revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8067 (m-80) cc_final: 0.7689 (m-80) REVERT: C 332 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7028 (mm) REVERT: C 340 GLU cc_start: 0.8141 (mp0) cc_final: 0.7826 (mp0) REVERT: C 396 TYR cc_start: 0.8128 (m-80) cc_final: 0.7727 (m-80) REVERT: C 537 LYS cc_start: 0.7456 (mtpp) cc_final: 0.7168 (tppt) REVERT: C 674 TYR cc_start: 0.8776 (t80) cc_final: 0.8346 (t80) REVERT: C 675 GLN cc_start: 0.7309 (pp30) cc_final: 0.6595 (pp30) REVERT: C 1073 LYS cc_start: 0.7862 (ptmm) cc_final: 0.7212 (mtpt) REVERT: B 224 GLU cc_start: 0.8475 (mp0) cc_final: 0.8029 (mp0) REVERT: B 422 ASN cc_start: 0.8214 (m110) cc_final: 0.7836 (m-40) REVERT: B 646 ARG cc_start: 0.7910 (mtp180) cc_final: 0.7325 (ttt90) REVERT: B 1107 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7167 (mmm160) REVERT: A 53 ASP cc_start: 0.7321 (t0) cc_final: 0.6949 (t0) REVERT: A 201 PHE cc_start: 0.5698 (m-80) cc_final: 0.5461 (m-80) REVERT: A 224 GLU cc_start: 0.6647 (mp0) cc_final: 0.6216 (mp0) REVERT: A 287 ASP cc_start: 0.7285 (m-30) cc_final: 0.6966 (m-30) REVERT: A 811 LYS cc_start: 0.7328 (mmtm) cc_final: 0.6470 (tttp) REVERT: A 904 TYR cc_start: 0.7822 (m-10) cc_final: 0.7426 (m-10) outliers start: 40 outliers final: 29 residues processed: 256 average time/residue: 0.3621 time to fit residues: 150.7765 Evaluate side-chains 251 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 3.108 ------------------------------------------------------------------------------- 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 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 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 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 752 LEU 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 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 114 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 295 optimal weight: 0.8980 chunk 271 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN B 339 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A1083 HIS A1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.180502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.141068 restraints weight = 29200.747| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.78 r_work: 0.3166 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 25424 Z= 0.232 Angle : 0.627 9.256 34662 Z= 0.321 Chirality : 0.047 0.254 4009 Planarity : 0.004 0.048 4424 Dihedral : 6.019 59.712 3951 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.47 % Allowed : 12.23 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 3081 helix: 1.65 (0.20), residues: 673 sheet: -0.29 (0.20), residues: 637 loop : -1.54 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.006 0.001 HIS C1058 PHE 0.030 0.002 PHE A 392 TYR 0.015 0.002 TYR C 266 ARG 0.005 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 29) link_NAG-ASN : angle 2.34450 ( 87) hydrogen bonds : bond 0.06153 ( 882) hydrogen bonds : angle 4.98171 ( 2466) SS BOND : bond 0.00468 ( 41) SS BOND : angle 2.20245 ( 82) covalent geometry : bond 0.00576 (25354) covalent geometry : angle 0.60798 (34493) *********************** 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 291 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 224 time to evaluate : 2.705 Fit side-chains revert: symmetry clash REVERT: C 396 TYR cc_start: 0.8102 (m-80) cc_final: 0.7754 (m-80) REVERT: C 537 LYS cc_start: 0.7688 (mtpp) cc_final: 0.7423 (tppt) REVERT: C 564 GLN cc_start: 0.8353 (tp40) cc_final: 0.7885 (tp40) REVERT: C 675 GLN cc_start: 0.7349 (pp30) cc_final: 0.6647 (pp30) REVERT: B 125 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7735 (m110) REVERT: B 224 GLU cc_start: 0.8437 (mp0) cc_final: 0.7972 (mp0) REVERT: B 422 ASN cc_start: 0.8262 (m110) cc_final: 0.7903 (m-40) REVERT: B 646 ARG cc_start: 0.7838 (mtp180) cc_final: 0.7284 (ttt90) REVERT: B 1107 ARG cc_start: 0.7813 (mtt180) cc_final: 0.7173 (mmm160) REVERT: A 53 ASP cc_start: 0.7239 (t0) cc_final: 0.6820 (t0) REVERT: A 287 ASP cc_start: 0.7203 (m-30) cc_final: 0.6850 (m-30) REVERT: A 675 GLN cc_start: 0.5746 (mm-40) cc_final: 0.5494 (tt0) REVERT: A 811 LYS cc_start: 0.7513 (mmtm) cc_final: 0.6536 (tttm) REVERT: A 904 TYR cc_start: 0.7566 (m-10) cc_final: 0.7079 (m-10) outliers start: 67 outliers final: 50 residues processed: 275 average time/residue: 0.3378 time to fit residues: 151.1264 Evaluate side-chains 263 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 212 time to evaluate : 2.498 ------------------------------------------------------------------------------- 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 312 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 881 THR Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain B residue 87 ASN 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 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 752 LEU 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 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 620 VAL Chi-restraints excluded: chain A residue 714 ILE 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 878 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 0.0040 chunk 277 optimal weight: 0.9990 chunk 287 optimal weight: 0.7980 chunk 296 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A1083 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.173565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.131086 restraints weight = 29809.125| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.20 r_work: 0.3150 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2191 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= 0.113 Angle : 0.538 8.063 34662 Z= 0.274 Chirality : 0.043 0.252 4009 Planarity : 0.004 0.049 4424 Dihedral : 5.526 58.465 3951 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.84 % Allowed : 13.22 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.15), residues: 3081 helix: 1.95 (0.20), residues: 684 sheet: -0.20 (0.20), residues: 670 loop : -1.48 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.004 0.001 HIS A 339 PHE 0.020 0.001 PHE A 392 TYR 0.017 0.001 TYR A1138 ARG 0.005 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 29) link_NAG-ASN : angle 2.18138 ( 87) hydrogen bonds : bond 0.04805 ( 882) hydrogen bonds : angle 4.69427 ( 2466) SS BOND : bond 0.00293 ( 41) SS BOND : angle 1.78998 ( 82) covalent geometry : bond 0.00261 (25354) covalent geometry : angle 0.52087 (34493) *********************** 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 279 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 2.322 Fit side-chains revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8043 (m-80) cc_final: 0.7690 (m-80) REVERT: C 340 GLU cc_start: 0.8150 (mp0) cc_final: 0.7818 (mp0) REVERT: C 367 VAL cc_start: 0.8766 (m) cc_final: 0.8525 (p) REVERT: C 396 TYR cc_start: 0.8099 (m-80) cc_final: 0.7652 (m-80) REVERT: C 537 LYS cc_start: 0.7598 (mtpp) cc_final: 0.7306 (tppt) REVERT: C 564 GLN cc_start: 0.8299 (tp40) cc_final: 0.7818 (tp40) REVERT: C 674 TYR cc_start: 0.8640 (t80) cc_final: 0.8277 (t80) REVERT: C 675 GLN cc_start: 0.7119 (pp30) cc_final: 0.6490 (pp30) REVERT: C 1073 LYS cc_start: 0.7680 (ptmm) cc_final: 0.7046 (mtpt) REVERT: B 224 GLU cc_start: 0.8425 (mp0) cc_final: 0.8004 (mp0) REVERT: B 383 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8268 (p) REVERT: B 422 ASN cc_start: 0.8381 (m110) cc_final: 0.7938 (m-40) REVERT: B 646 ARG cc_start: 0.7782 (mtp180) cc_final: 0.7180 (ttt90) REVERT: B 1107 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7087 (mmm160) REVERT: A 53 ASP cc_start: 0.7067 (t0) cc_final: 0.6564 (t0) REVERT: A 287 ASP cc_start: 0.7175 (m-30) cc_final: 0.6796 (m-30) REVERT: A 675 GLN cc_start: 0.5757 (mm-40) cc_final: 0.5456 (tt0) REVERT: A 811 LYS cc_start: 0.7356 (mmtm) cc_final: 0.6492 (tttm) REVERT: A 904 TYR cc_start: 0.7570 (m-10) cc_final: 0.7149 (m-10) outliers start: 50 outliers final: 37 residues processed: 265 average time/residue: 0.3468 time to fit residues: 149.5915 Evaluate side-chains 256 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 218 time to evaluate : 2.823 ------------------------------------------------------------------------------- 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 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 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 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 588 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 934 ILE 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 547 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 153 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 272 optimal weight: 3.9990 chunk 133 optimal weight: 0.3980 chunk 218 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 chunk 301 optimal weight: 1.9990 chunk 274 optimal weight: 0.5980 overall best weight: 0.5340 ------------------------------------------------------------------------------- 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** C 544 ASN B 125 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.185986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.147445 restraints weight = 29032.276| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.53 r_work: 0.3286 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25424 Z= 0.102 Angle : 0.525 7.665 34662 Z= 0.267 Chirality : 0.043 0.244 4009 Planarity : 0.004 0.047 4424 Dihedral : 5.288 57.782 3951 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.51 % Allowed : 13.81 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3081 helix: 2.18 (0.20), residues: 677 sheet: -0.08 (0.21), residues: 615 loop : -1.43 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 886 HIS 0.002 0.000 HIS B1083 PHE 0.016 0.001 PHE A 43 TYR 0.017 0.001 TYR A1138 ARG 0.005 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 29) link_NAG-ASN : angle 2.11182 ( 87) hydrogen bonds : bond 0.04464 ( 882) hydrogen bonds : angle 4.57457 ( 2466) SS BOND : bond 0.00270 ( 41) SS BOND : angle 1.69284 ( 82) covalent geometry : bond 0.00229 (25354) covalent geometry : angle 0.50927 (34493) *********************** 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 268 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 2.546 Fit side-chains revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8048 (m-80) cc_final: 0.7779 (m-80) REVERT: C 367 VAL cc_start: 0.8890 (m) cc_final: 0.8627 (p) REVERT: C 396 TYR cc_start: 0.8193 (m-80) cc_final: 0.7790 (m-80) REVERT: C 537 LYS cc_start: 0.7569 (mtpp) cc_final: 0.7282 (tppt) REVERT: C 674 TYR cc_start: 0.8742 (t80) cc_final: 0.8386 (t80) REVERT: C 675 GLN cc_start: 0.7306 (pp30) cc_final: 0.6672 (pp30) REVERT: C 902 MET cc_start: 0.8970 (tpt) cc_final: 0.8677 (mmm) REVERT: C 1073 LYS cc_start: 0.7858 (ptmm) cc_final: 0.7264 (mtpt) REVERT: B 224 GLU cc_start: 0.8506 (mp0) cc_final: 0.8140 (mp0) REVERT: B 383 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8302 (p) REVERT: B 422 ASN cc_start: 0.8439 (m110) cc_final: 0.8123 (m-40) REVERT: B 646 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7228 (ttt90) REVERT: B 1107 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7162 (mmm160) REVERT: A 53 ASP cc_start: 0.7244 (t0) cc_final: 0.6750 (t0) REVERT: A 287 ASP cc_start: 0.7361 (m-30) cc_final: 0.6994 (m-30) REVERT: A 811 LYS cc_start: 0.7425 (mmtm) cc_final: 0.6527 (tttm) REVERT: A 904 TYR cc_start: 0.7750 (m-10) cc_final: 0.7355 (m-10) outliers start: 41 outliers final: 38 residues processed: 254 average time/residue: 0.3418 time to fit residues: 141.6721 Evaluate side-chains 249 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 2.554 ------------------------------------------------------------------------------- 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 878 LEU 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 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 420 ASP 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 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 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 547 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 119 optimal weight: 4.9990 chunk 234 optimal weight: 0.5980 chunk 224 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 270 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 236 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 422 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 = 0.4048 r_free = 0.4048 target = 0.185762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.146559 restraints weight = 29129.552| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.56 r_work: 0.3153 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2269 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= 0.113 Angle : 0.531 11.654 34662 Z= 0.268 Chirality : 0.043 0.237 4009 Planarity : 0.004 0.047 4424 Dihedral : 5.167 57.355 3951 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.92 % Allowed : 13.70 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 3081 helix: 2.10 (0.20), residues: 684 sheet: -0.07 (0.21), residues: 622 loop : -1.44 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.000 HIS B1083 PHE 0.018 0.001 PHE A 43 TYR 0.013 0.001 TYR B1067 ARG 0.005 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 29) link_NAG-ASN : angle 2.07071 ( 87) hydrogen bonds : bond 0.04514 ( 882) hydrogen bonds : angle 4.54645 ( 2466) SS BOND : bond 0.00291 ( 41) SS BOND : angle 1.70637 ( 82) covalent geometry : bond 0.00264 (25354) covalent geometry : angle 0.51515 (34493) *********************** 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 271 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 219 time to evaluate : 2.460 Fit side-chains revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8045 (m-80) cc_final: 0.7740 (m-80) REVERT: C 367 VAL cc_start: 0.8783 (m) cc_final: 0.8517 (p) REVERT: C 396 TYR cc_start: 0.8145 (m-80) cc_final: 0.7732 (m-80) REVERT: C 451 TYR cc_start: 0.7043 (m-10) cc_final: 0.6783 (m-10) REVERT: C 537 LYS cc_start: 0.7544 (mtpp) cc_final: 0.7223 (tppt) REVERT: C 564 GLN cc_start: 0.8190 (tp40) cc_final: 0.7726 (tp40) REVERT: C 674 TYR cc_start: 0.8741 (t80) cc_final: 0.8363 (t80) REVERT: C 675 GLN cc_start: 0.7133 (pp30) cc_final: 0.6484 (pp30) REVERT: C 902 MET cc_start: 0.9023 (tpt) cc_final: 0.8622 (tpt) REVERT: C 1073 LYS cc_start: 0.7848 (ptmm) cc_final: 0.7225 (mtpt) REVERT: B 224 GLU cc_start: 0.8470 (mp0) cc_final: 0.8056 (mp0) REVERT: B 383 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8285 (p) REVERT: B 422 ASN cc_start: 0.8435 (m110) cc_final: 0.8060 (m-40) REVERT: B 646 ARG cc_start: 0.7870 (mtp180) cc_final: 0.7212 (ttt90) REVERT: A 53 ASP cc_start: 0.7219 (t0) cc_final: 0.6718 (t0) REVERT: A 224 GLU cc_start: 0.6602 (mp0) cc_final: 0.6116 (mp0) REVERT: A 287 ASP cc_start: 0.7345 (m-30) cc_final: 0.6962 (m-30) REVERT: A 675 GLN cc_start: 0.5738 (mm-40) cc_final: 0.5374 (tt0) REVERT: A 811 LYS cc_start: 0.7393 (mmtm) cc_final: 0.6485 (tttm) REVERT: A 904 TYR cc_start: 0.7736 (m-10) cc_final: 0.7423 (m-10) outliers start: 52 outliers final: 46 residues processed: 255 average time/residue: 0.3488 time to fit residues: 147.2321 Evaluate side-chains 261 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 2.437 ------------------------------------------------------------------------------- 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 620 VAL Chi-restraints excluded: chain C residue 878 LEU 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 420 ASP 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 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 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 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 620 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 881 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 235 optimal weight: 0.7980 chunk 219 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 9 optimal weight: 0.0170 chunk 203 optimal weight: 0.6980 chunk 310 optimal weight: 1.9990 chunk 264 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 228 optimal weight: 10.0000 overall best weight: 0.6620 ------------------------------------------------------------------------------- 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 422 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 = 0.4054 r_free = 0.4054 target = 0.186443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.146932 restraints weight = 29049.892| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.57 r_work: 0.3163 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25424 Z= 0.105 Angle : 0.526 9.528 34662 Z= 0.266 Chirality : 0.043 0.233 4009 Planarity : 0.004 0.046 4424 Dihedral : 5.071 57.171 3951 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.84 % Allowed : 13.92 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3081 helix: 2.10 (0.20), residues: 690 sheet: -0.03 (0.21), residues: 619 loop : -1.41 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.003 0.000 HIS B1083 PHE 0.017 0.001 PHE A 43 TYR 0.020 0.001 TYR A1138 ARG 0.005 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 29) link_NAG-ASN : angle 2.02359 ( 87) hydrogen bonds : bond 0.04364 ( 882) hydrogen bonds : angle 4.50085 ( 2466) SS BOND : bond 0.00282 ( 41) SS BOND : angle 1.66691 ( 82) covalent geometry : bond 0.00243 (25354) covalent geometry : angle 0.51049 (34493) ********************** 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 269 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 200 TYR cc_start: 0.8016 (m-80) cc_final: 0.7733 (m-80) REVERT: C 367 VAL cc_start: 0.8750 (m) cc_final: 0.8480 (p) REVERT: C 396 TYR cc_start: 0.8124 (m-80) cc_final: 0.7711 (m-80) REVERT: C 451 TYR cc_start: 0.7027 (m-10) cc_final: 0.6775 (m-10) REVERT: C 458 LYS cc_start: 0.7169 (tttt) cc_final: 0.6679 (mttp) REVERT: C 537 LYS cc_start: 0.7526 (mtpp) cc_final: 0.7205 (tppt) REVERT: C 564 GLN cc_start: 0.8175 (tp40) cc_final: 0.7704 (tp40) REVERT: C 674 TYR cc_start: 0.8716 (t80) cc_final: 0.8344 (t80) REVERT: C 675 GLN cc_start: 0.7098 (pp30) cc_final: 0.6457 (pp30) REVERT: C 902 MET cc_start: 0.8989 (tpt) cc_final: 0.8697 (mmm) REVERT: C 1073 LYS cc_start: 0.7819 (ptmm) cc_final: 0.7204 (mtpt) REVERT: B 224 GLU cc_start: 0.8464 (mp0) cc_final: 0.8046 (mp0) REVERT: B 383 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8265 (p) REVERT: B 422 ASN cc_start: 0.8441 (m110) cc_final: 0.8063 (m-40) REVERT: B 646 ARG cc_start: 0.7851 (mtp180) cc_final: 0.7191 (ttt90) REVERT: A 53 ASP cc_start: 0.7171 (t0) cc_final: 0.6771 (t0) REVERT: A 224 GLU cc_start: 0.6597 (mp0) cc_final: 0.6114 (mp0) REVERT: A 287 ASP cc_start: 0.7346 (m-30) cc_final: 0.6961 (m-30) REVERT: A 811 LYS cc_start: 0.7384 (mmtm) cc_final: 0.6508 (tttm) REVERT: A 904 TYR cc_start: 0.7795 (m-10) cc_final: 0.7484 (m-10) outliers start: 50 outliers final: 44 residues processed: 253 average time/residue: 0.3331 time to fit residues: 138.1233 Evaluate side-chains 260 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 2.675 ------------------------------------------------------------------------------- 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 588 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 878 LEU 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 383 SER 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 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 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 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 620 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 881 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 76 optimal weight: 0.6980 chunk 249 optimal weight: 2.9990 chunk 152 optimal weight: 0.3980 chunk 28 optimal weight: 7.9990 chunk 295 optimal weight: 2.9990 chunk 262 optimal weight: 0.0050 chunk 227 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 143 optimal weight: 0.0570 chunk 162 optimal weight: 1.9990 chunk 292 optimal weight: 0.0070 overall best weight: 0.2330 ------------------------------------------------------------------------------- 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** C 955 ASN B 125 ASN B 422 ASN B 949 GLN A 955 ASN A1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.188051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.149274 restraints weight = 29228.769| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.45 r_work: 0.3223 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25424 Z= 0.089 Angle : 0.504 7.865 34662 Z= 0.255 Chirality : 0.043 0.233 4009 Planarity : 0.003 0.047 4424 Dihedral : 4.762 55.808 3951 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.14 % Allowed : 14.59 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3081 helix: 2.26 (0.20), residues: 694 sheet: 0.04 (0.21), residues: 631 loop : -1.36 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.000 HIS A1048 PHE 0.016 0.001 PHE A 43 TYR 0.018 0.001 TYR A1138 ARG 0.005 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 29) link_NAG-ASN : angle 1.89713 ( 87) hydrogen bonds : bond 0.03698 ( 882) hydrogen bonds : angle 4.35065 ( 2466) SS BOND : bond 0.00248 ( 41) SS BOND : angle 1.44194 ( 82) covalent geometry : bond 0.00194 (25354) covalent geometry : angle 0.49069 (34493) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13158.19 seconds wall clock time: 225 minutes 52.84 seconds (13552.84 seconds total)