Starting phenix.real_space_refine on Sat Jun 21 15:10:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ayy_44002/06_2025/9ayy_44002_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ayy_44002/06_2025/9ayy_44002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ayy_44002/06_2025/9ayy_44002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ayy_44002/06_2025/9ayy_44002.map" model { file = "/net/cci-nas-00/data/ceres_data/9ayy_44002/06_2025/9ayy_44002_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ayy_44002/06_2025/9ayy_44002_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.047 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 15840 2.51 5 N 4095 2.21 5 O 4764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24813 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8131 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "B" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8131 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "C" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8131 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 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 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 15.53, per 1000 atoms: 0.63 Number of scatterers: 24813 At special positions: 0 Unit cell: (137.16, 129.6, 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 4764 8.00 N 4095 7.00 C 15840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 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 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 234 " " NAG C1310 " - " ASN C 801 " Time building additional restraints: 6.10 Conformation dependent library (CDL) restraints added in 3.4 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 50 sheets defined 25.4% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.651A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.774A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 842 removed outlier: 3.573A pdb=" N GLY A 842 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.550A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.517A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.544A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.881A 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: 3.611A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.904A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.531A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.925A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 368' Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.775A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.504A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.975A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.835A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 842 removed outlier: 3.583A pdb=" N CYS B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.556A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.600A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.733A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.507A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.593A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.515A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.829A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 removed outlier: 3.829A pdb=" N MET C 177 " --> pdb=" O GLN C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.895A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN C 343 " --> pdb=" O HIS C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 338 through 343' Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.813A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.634A pdb=" N HIS C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 506' Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.672A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.811A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.739A 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 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.553A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.629A 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: 3.584A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.896A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.878A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.952A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.952A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.019A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.947A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.199A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.498A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.257A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.534A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.519A pdb=" N VAL A 551 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.020A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.743A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 722 removed outlier: 6.149A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.665A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 25 through 30 removed outlier: 8.381A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.511A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.018A 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 removed outlier: 6.231A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.218A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.656A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.656A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.997A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.518A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.527A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 584 through 586 removed outlier: 7.139A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.130A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.589A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.626A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.153A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.623A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 25 through 30 removed outlier: 7.859A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.001A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'C' and resid 117 through 120 removed outlier: 3.695A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.128A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 394 through 395 removed outlier: 4.336A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 398 through 402 Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.704A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.620A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.070A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.515A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.024A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.712A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 947 hydrogen bonds defined for protein. 2628 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: 11.21 Time building geometry restraints manager: 7.26 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: 7925 1.35 - 1.47: 6446 1.47 - 1.60: 10862 1.60 - 1.72: 0 1.72 - 1.85: 141 Bond restraints: 25374 Sorted by residual: bond pdb=" CG PRO B 57 " pdb=" CD PRO B 57 " ideal model delta sigma weight residual 1.503 1.355 0.148 3.40e-02 8.65e+02 1.88e+01 bond pdb=" C VAL C 620 " pdb=" N PRO C 621 " ideal model delta sigma weight residual 1.334 1.407 -0.073 2.34e-02 1.83e+03 9.63e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.85e+00 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.95e+00 ... (remaining 25369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 34220 2.96 - 5.92: 256 5.92 - 8.88: 35 8.88 - 11.84: 8 11.84 - 14.80: 2 Bond angle restraints: 34521 Sorted by residual: angle pdb=" N PRO B 57 " pdb=" CD PRO B 57 " pdb=" CG PRO B 57 " ideal model delta sigma weight residual 103.20 90.43 12.77 1.50e+00 4.44e-01 7.25e+01 angle pdb=" CA PRO B 57 " pdb=" CB PRO B 57 " pdb=" CG PRO B 57 " ideal model delta sigma weight residual 104.50 93.04 11.46 1.90e+00 2.77e-01 3.64e+01 angle pdb=" C GLY C 744 " pdb=" N ASP C 745 " pdb=" CA ASP C 745 " ideal model delta sigma weight residual 121.54 131.33 -9.79 1.91e+00 2.74e-01 2.62e+01 angle pdb=" CA PRO B 57 " pdb=" N PRO B 57 " pdb=" CD PRO B 57 " ideal model delta sigma weight residual 112.00 105.08 6.92 1.40e+00 5.10e-01 2.44e+01 angle pdb=" C ASN C 87 " pdb=" N ASP C 88 " pdb=" CA ASP C 88 " ideal model delta sigma weight residual 121.54 130.74 -9.20 1.91e+00 2.74e-01 2.32e+01 ... (remaining 34516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13976 17.94 - 35.87: 1267 35.87 - 53.81: 216 53.81 - 71.75: 51 71.75 - 89.69: 33 Dihedral angle restraints: 15543 sinusoidal: 6438 harmonic: 9105 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -175.69 89.69 1 1.00e+01 1.00e-02 9.55e+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 -4.24 -81.76 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 -146.72 60.72 1 1.00e+01 1.00e-02 4.90e+01 ... (remaining 15540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3664 0.097 - 0.193: 336 0.193 - 0.290: 11 0.290 - 0.386: 2 0.386 - 0.483: 1 Chirality restraints: 4014 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+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 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 4011 not shown) Planarity restraints: 4455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO B 521 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 453 " -0.015 2.00e-02 2.50e+03 1.84e-02 6.80e+00 pdb=" CG TYR B 453 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B 453 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 453 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR B 453 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 453 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 453 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 453 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.77e+00 pdb=" N PRO C 521 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.036 5.00e-02 4.00e+02 ... (remaining 4452 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 6622 2.81 - 3.33: 19649 3.33 - 3.85: 39747 3.85 - 4.38: 44161 4.38 - 4.90: 80156 Nonbonded interactions: 190335 Sorted by model distance: nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.284 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.297 3.040 nonbonded pdb=" O THR C 109 " pdb=" OG SER C 116 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.323 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" OD2 ASP B 53 " model vdw 2.338 3.040 ... (remaining 190330 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.060 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 61.030 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 25445 Z= 0.210 Angle : 0.753 17.831 34693 Z= 0.386 Chirality : 0.053 0.483 4014 Planarity : 0.006 0.068 4425 Dihedral : 14.355 86.199 9558 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.28 (0.14), residues: 3081 helix: 0.10 (0.19), residues: 621 sheet: 0.05 (0.21), residues: 615 loop : -1.57 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 886 HIS 0.007 0.001 HIS B1101 PHE 0.030 0.002 PHE C 906 TYR 0.046 0.001 TYR B 453 ARG 0.007 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00710 ( 30) link_NAG-ASN : angle 3.00711 ( 90) hydrogen bonds : bond 0.22499 ( 926) hydrogen bonds : angle 8.22184 ( 2628) SS BOND : bond 0.00506 ( 41) SS BOND : angle 2.13779 ( 82) covalent geometry : bond 0.00460 (25374) covalent geometry : angle 0.73131 (34521) *********************** 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 183 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 2.506 Fit side-chains revert: symmetry clash REVERT: A 170 TYR cc_start: 0.6321 (t80) cc_final: 0.5984 (t80) REVERT: A 237 ARG cc_start: 0.7130 (ptp-110) cc_final: 0.6269 (mtm110) REVERT: B 57 PRO cc_start: 0.4843 (Cg_endo) cc_final: 0.4639 (Cg_exo) REVERT: C 355 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7269 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.3550 time to fit residues: 107.3499 Evaluate side-chains 147 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 131 optimal weight: 0.0470 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 0.0870 chunk 126 optimal weight: 3.9990 chunk 244 optimal weight: 0.0010 chunk 94 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 283 optimal weight: 0.7980 overall best weight: 0.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 422 ASN A 613 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN C 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.220058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133099 restraints weight = 28862.391| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.11 r_work: 0.3364 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 25445 Z= 0.100 Angle : 0.516 13.550 34693 Z= 0.268 Chirality : 0.043 0.348 4014 Planarity : 0.004 0.053 4425 Dihedral : 5.941 55.664 3972 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.33 % Allowed : 5.41 % Favored : 94.25 % 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: -0.43 (0.15), residues: 3081 helix: 1.46 (0.20), residues: 648 sheet: 0.22 (0.20), residues: 681 loop : -1.21 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.003 0.001 HIS B 52 PHE 0.019 0.001 PHE A 592 TYR 0.015 0.001 TYR C1067 ARG 0.003 0.000 ARG C 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 30) link_NAG-ASN : angle 2.25877 ( 90) hydrogen bonds : bond 0.04704 ( 926) hydrogen bonds : angle 5.77393 ( 2628) SS BOND : bond 0.00269 ( 41) SS BOND : angle 1.46109 ( 82) covalent geometry : bond 0.00211 (25374) covalent geometry : angle 0.49887 (34521) *********************** 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 175 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 166 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7414 (ptp-110) cc_final: 0.6536 (ptp90) REVERT: A 955 ASN cc_start: 0.7433 (m110) cc_final: 0.7218 (m110) REVERT: B 613 GLN cc_start: 0.7967 (mt0) cc_final: 0.7667 (mt0) REVERT: B 616 ASN cc_start: 0.6764 (p0) cc_final: 0.6088 (t0) REVERT: C 355 ARG cc_start: 0.7895 (ttm110) cc_final: 0.7048 (mmm-85) REVERT: C 356 LYS cc_start: 0.7167 (tptt) cc_final: 0.6928 (tptt) REVERT: C 754 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8053 (mp) outliers start: 9 outliers final: 3 residues processed: 167 average time/residue: 0.3482 time to fit residues: 96.8711 Evaluate side-chains 148 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 308 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 chunk 276 optimal weight: 0.0040 chunk 304 optimal weight: 3.9990 chunk 235 optimal weight: 0.0470 chunk 303 optimal weight: 0.6980 chunk 279 optimal weight: 1.9990 overall best weight: 1.1494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN C 394 ASN C1101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.216066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.131229 restraints weight = 28285.838| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.07 r_work: 0.3293 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25445 Z= 0.132 Angle : 0.517 13.057 34693 Z= 0.267 Chirality : 0.044 0.312 4014 Planarity : 0.003 0.047 4425 Dihedral : 5.544 59.773 3972 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.48 % Allowed : 7.92 % Favored : 91.60 % 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: -0.31 (0.15), residues: 3081 helix: 1.70 (0.20), residues: 664 sheet: 0.34 (0.20), residues: 646 loop : -1.22 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.003 0.001 HIS A1064 PHE 0.020 0.001 PHE C 906 TYR 0.019 0.001 TYR B1067 ARG 0.002 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 30) link_NAG-ASN : angle 2.17727 ( 90) hydrogen bonds : bond 0.05072 ( 926) hydrogen bonds : angle 5.32117 ( 2628) SS BOND : bond 0.00290 ( 41) SS BOND : angle 1.56557 ( 82) covalent geometry : bond 0.00312 (25374) covalent geometry : angle 0.50046 (34521) *********************** 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 170 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7478 (ptp-110) cc_final: 0.6625 (ptp90) REVERT: A 646 ARG cc_start: 0.7338 (mtm180) cc_final: 0.6889 (mtp180) REVERT: A 955 ASN cc_start: 0.7497 (m110) cc_final: 0.7273 (m110) REVERT: B 206 LYS cc_start: 0.5016 (ttpp) cc_final: 0.4526 (tptm) REVERT: B 592 PHE cc_start: 0.6200 (p90) cc_final: 0.5968 (p90) REVERT: B 616 ASN cc_start: 0.6809 (p0) cc_final: 0.6278 (t0) REVERT: B 904 TYR cc_start: 0.7475 (m-10) cc_final: 0.7209 (m-80) REVERT: C 356 LYS cc_start: 0.7306 (tptt) cc_final: 0.6969 (tptm) outliers start: 13 outliers final: 9 residues processed: 165 average time/residue: 0.3454 time to fit residues: 94.8844 Evaluate side-chains 152 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 214 optimal weight: 0.0970 chunk 18 optimal weight: 10.0000 chunk 188 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 273 optimal weight: 0.6980 chunk 211 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 240 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN C1101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.218585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131719 restraints weight = 28949.653| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.06 r_work: 0.3326 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25445 Z= 0.100 Angle : 0.478 12.927 34693 Z= 0.245 Chirality : 0.043 0.307 4014 Planarity : 0.003 0.045 4425 Dihedral : 5.089 54.990 3972 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.85 % Allowed : 8.99 % Favored : 90.17 % 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: -0.14 (0.15), residues: 3081 helix: 1.99 (0.20), residues: 664 sheet: 0.36 (0.19), residues: 669 loop : -1.16 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.003 0.000 HIS B 52 PHE 0.012 0.001 PHE A 135 TYR 0.016 0.001 TYR B1067 ARG 0.002 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 30) link_NAG-ASN : angle 2.08707 ( 90) hydrogen bonds : bond 0.04339 ( 926) hydrogen bonds : angle 4.99673 ( 2628) SS BOND : bond 0.00256 ( 41) SS BOND : angle 1.46409 ( 82) covalent geometry : bond 0.00228 (25374) covalent geometry : angle 0.46148 (34521) *********************** 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 184 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7415 (ptp-110) cc_final: 0.6796 (mtm110) REVERT: A 646 ARG cc_start: 0.7347 (mtm180) cc_final: 0.6930 (mtp180) REVERT: A 814 LYS cc_start: 0.8374 (mmtm) cc_final: 0.7282 (ptmm) REVERT: B 206 LYS cc_start: 0.4999 (ttpp) cc_final: 0.4501 (tptm) REVERT: B 592 PHE cc_start: 0.6136 (p90) cc_final: 0.5899 (p90) REVERT: B 616 ASN cc_start: 0.6801 (p0) cc_final: 0.6271 (t0) REVERT: B 904 TYR cc_start: 0.7367 (m-10) cc_final: 0.7137 (m-80) REVERT: C 356 LYS cc_start: 0.7367 (tptt) cc_final: 0.7023 (tptm) outliers start: 23 outliers final: 14 residues processed: 177 average time/residue: 0.3337 time to fit residues: 98.6054 Evaluate side-chains 168 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 224 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 242 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 294 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 280 optimal weight: 0.0570 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C1101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.216469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.128993 restraints weight = 28904.912| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.31 r_work: 0.3276 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25445 Z= 0.120 Angle : 0.496 12.832 34693 Z= 0.254 Chirality : 0.043 0.305 4014 Planarity : 0.003 0.043 4425 Dihedral : 4.975 53.483 3972 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.96 % Allowed : 10.09 % Favored : 88.95 % 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: -0.11 (0.15), residues: 3081 helix: 2.10 (0.20), residues: 659 sheet: 0.36 (0.19), residues: 669 loop : -1.16 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS A1064 PHE 0.020 0.001 PHE C 906 TYR 0.017 0.001 TYR B1067 ARG 0.002 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 30) link_NAG-ASN : angle 2.12992 ( 90) hydrogen bonds : bond 0.04638 ( 926) hydrogen bonds : angle 4.90872 ( 2628) SS BOND : bond 0.00312 ( 41) SS BOND : angle 1.65645 ( 82) covalent geometry : bond 0.00285 (25374) covalent geometry : angle 0.47818 (34521) *********************** 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 180 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 2.699 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7453 (ptp-110) cc_final: 0.6780 (mtm110) REVERT: A 646 ARG cc_start: 0.7370 (mtm180) cc_final: 0.6934 (mtp180) REVERT: A 814 LYS cc_start: 0.8425 (mmtm) cc_final: 0.7351 (ptmm) REVERT: A 955 ASN cc_start: 0.7769 (m-40) cc_final: 0.7529 (m110) REVERT: A 1107 ARG cc_start: 0.7983 (mtp180) cc_final: 0.7705 (mtp180) REVERT: B 49 HIS cc_start: 0.7608 (t-90) cc_final: 0.7351 (t-170) REVERT: B 616 ASN cc_start: 0.6555 (p0) cc_final: 0.5754 (t0) REVERT: B 904 TYR cc_start: 0.7540 (m-10) cc_final: 0.7235 (m-80) REVERT: C 356 LYS cc_start: 0.7358 (tptt) cc_final: 0.7030 (tptm) outliers start: 26 outliers final: 20 residues processed: 173 average time/residue: 0.3406 time to fit residues: 97.8585 Evaluate side-chains 169 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 202 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 263 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 36 optimal weight: 30.0000 chunk 120 optimal weight: 3.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 901 GLN B 196 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 506 GLN C 394 ASN C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.212074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126495 restraints weight = 28641.531| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.09 r_work: 0.3215 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 25445 Z= 0.281 Angle : 0.655 12.872 34693 Z= 0.337 Chirality : 0.049 0.260 4014 Planarity : 0.004 0.052 4425 Dihedral : 5.829 54.033 3972 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.29 % Allowed : 10.83 % Favored : 87.88 % 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: -0.54 (0.14), residues: 3081 helix: 1.60 (0.20), residues: 646 sheet: 0.13 (0.19), residues: 667 loop : -1.36 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 886 HIS 0.008 0.001 HIS A1064 PHE 0.041 0.002 PHE C 906 TYR 0.024 0.002 TYR B 453 ARG 0.005 0.001 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 30) link_NAG-ASN : angle 2.44803 ( 90) hydrogen bonds : bond 0.06781 ( 926) hydrogen bonds : angle 5.30973 ( 2628) SS BOND : bond 0.00446 ( 41) SS BOND : angle 2.34885 ( 82) covalent geometry : bond 0.00695 (25374) covalent geometry : angle 0.63411 (34521) *********************** 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 194 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 2.541 Fit side-chains REVERT: A 237 ARG cc_start: 0.7474 (ptp-110) cc_final: 0.6795 (mtm110) REVERT: A 646 ARG cc_start: 0.7391 (mtm180) cc_final: 0.6989 (mtp180) REVERT: A 748 GLU cc_start: 0.8140 (mp0) cc_final: 0.7889 (mp0) REVERT: A 994 ASP cc_start: 0.8209 (t0) cc_final: 0.7987 (t0) REVERT: A 1107 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7682 (mtp180) REVERT: B 449 TYR cc_start: 0.6558 (m-80) cc_final: 0.6276 (m-80) REVERT: B 616 ASN cc_start: 0.6541 (p0) cc_final: 0.6026 (t0) REVERT: B 902 MET cc_start: 0.8824 (tpt) cc_final: 0.8364 (tpt) REVERT: B 904 TYR cc_start: 0.7616 (m-10) cc_final: 0.7315 (m-80) REVERT: B 934 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8055 (tt) REVERT: C 326 ILE cc_start: 0.5858 (mt) cc_final: 0.5493 (pt) REVERT: C 356 LYS cc_start: 0.7445 (tptt) cc_final: 0.7176 (tptm) REVERT: C 573 THR cc_start: 0.8429 (m) cc_final: 0.8150 (p) REVERT: C 934 ILE cc_start: 0.7851 (tp) cc_final: 0.7544 (pt) REVERT: C 977 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7822 (mp) outliers start: 35 outliers final: 25 residues processed: 184 average time/residue: 0.3354 time to fit residues: 102.6180 Evaluate side-chains 178 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1055 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 138 optimal weight: 9.9990 chunk 203 optimal weight: 0.3980 chunk 45 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 170 optimal weight: 0.9980 chunk 192 optimal weight: 0.8980 chunk 292 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 243 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS C 394 ASN C 762 GLN C1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.216205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131982 restraints weight = 28720.388| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.18 r_work: 0.3265 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25445 Z= 0.110 Angle : 0.505 13.062 34693 Z= 0.260 Chirality : 0.044 0.295 4014 Planarity : 0.003 0.046 4425 Dihedral : 5.223 54.948 3972 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.10 % Allowed : 11.49 % Favored : 87.40 % 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: -0.22 (0.15), residues: 3081 helix: 2.07 (0.21), residues: 655 sheet: 0.25 (0.19), residues: 663 loop : -1.22 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS B 52 PHE 0.012 0.001 PHE B1121 TYR 0.027 0.001 TYR B 453 ARG 0.003 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 30) link_NAG-ASN : angle 2.19675 ( 90) hydrogen bonds : bond 0.04766 ( 926) hydrogen bonds : angle 4.89902 ( 2628) SS BOND : bond 0.00315 ( 41) SS BOND : angle 1.65273 ( 82) covalent geometry : bond 0.00250 (25374) covalent geometry : angle 0.48742 (34521) *********************** 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 196 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 2.588 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7363 (ptp-110) cc_final: 0.6702 (mtm110) REVERT: A 646 ARG cc_start: 0.7382 (mtm180) cc_final: 0.6979 (mtp180) REVERT: A 955 ASN cc_start: 0.7638 (m-40) cc_final: 0.7410 (m110) REVERT: A 1107 ARG cc_start: 0.7861 (mtp180) cc_final: 0.7402 (mtp180) REVERT: A 1128 VAL cc_start: 0.8358 (m) cc_final: 0.8034 (p) REVERT: B 449 TYR cc_start: 0.6494 (m-80) cc_final: 0.6183 (m-80) REVERT: B 616 ASN cc_start: 0.6516 (p0) cc_final: 0.5947 (t0) REVERT: B 904 TYR cc_start: 0.7568 (m-10) cc_final: 0.7211 (m-80) REVERT: B 935 GLN cc_start: 0.7425 (tm-30) cc_final: 0.7093 (tm-30) REVERT: C 326 ILE cc_start: 0.6114 (mt) cc_final: 0.5608 (pt) REVERT: C 356 LYS cc_start: 0.7351 (tptt) cc_final: 0.7073 (tptm) outliers start: 30 outliers final: 24 residues processed: 187 average time/residue: 0.3472 time to fit residues: 107.3546 Evaluate side-chains 183 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 963 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 166 optimal weight: 1.9990 chunk 44 optimal weight: 30.0000 chunk 49 optimal weight: 9.9990 chunk 304 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 262 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.214485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127176 restraints weight = 28566.475| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.22 r_work: 0.3255 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25445 Z= 0.159 Angle : 0.540 12.962 34693 Z= 0.278 Chirality : 0.045 0.279 4014 Planarity : 0.003 0.047 4425 Dihedral : 5.268 53.615 3972 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.10 % Allowed : 11.97 % Favored : 86.92 % 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: -0.25 (0.15), residues: 3081 helix: 2.00 (0.20), residues: 657 sheet: 0.22 (0.19), residues: 668 loop : -1.23 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS A1064 PHE 0.019 0.001 PHE C 906 TYR 0.026 0.001 TYR B 453 ARG 0.003 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 30) link_NAG-ASN : angle 2.25150 ( 90) hydrogen bonds : bond 0.05310 ( 926) hydrogen bonds : angle 4.94696 ( 2628) SS BOND : bond 0.00356 ( 41) SS BOND : angle 1.87305 ( 82) covalent geometry : bond 0.00386 (25374) covalent geometry : angle 0.52134 (34521) *********************** 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 185 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 2.535 Fit side-chains REVERT: A 237 ARG cc_start: 0.7309 (ptp-110) cc_final: 0.6704 (mtm110) REVERT: A 646 ARG cc_start: 0.7391 (mtm180) cc_final: 0.7001 (mtp180) REVERT: A 1107 ARG cc_start: 0.7846 (mtp180) cc_final: 0.7458 (mtp180) REVERT: A 1128 VAL cc_start: 0.8365 (m) cc_final: 0.8034 (p) REVERT: B 449 TYR cc_start: 0.6464 (m-80) cc_final: 0.6151 (m-80) REVERT: B 616 ASN cc_start: 0.6512 (p0) cc_final: 0.5958 (t0) REVERT: B 904 TYR cc_start: 0.7608 (m-10) cc_final: 0.7281 (m-80) REVERT: B 935 GLN cc_start: 0.7349 (tm-30) cc_final: 0.6984 (tm-30) REVERT: C 326 ILE cc_start: 0.5838 (mt) cc_final: 0.5538 (pt) REVERT: C 356 LYS cc_start: 0.7441 (tptt) cc_final: 0.7142 (tptm) outliers start: 30 outliers final: 25 residues processed: 178 average time/residue: 0.3388 time to fit residues: 99.9199 Evaluate side-chains 178 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 112 optimal weight: 20.0000 chunk 307 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 101 optimal weight: 0.0470 chunk 278 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 214 optimal weight: 0.9980 chunk 252 optimal weight: 9.9990 chunk 279 optimal weight: 0.5980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 49 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.216423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.130708 restraints weight = 28707.635| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.07 r_work: 0.3294 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25445 Z= 0.107 Angle : 0.501 13.059 34693 Z= 0.257 Chirality : 0.044 0.295 4014 Planarity : 0.003 0.045 4425 Dihedral : 5.050 54.287 3972 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.14 % Allowed : 12.12 % Favored : 86.74 % 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: -0.10 (0.15), residues: 3081 helix: 2.29 (0.20), residues: 650 sheet: 0.30 (0.19), residues: 665 loop : -1.18 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 353 HIS 0.003 0.001 HIS B 52 PHE 0.012 0.001 PHE A 592 TYR 0.028 0.001 TYR B 453 ARG 0.003 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 30) link_NAG-ASN : angle 2.14712 ( 90) hydrogen bonds : bond 0.04498 ( 926) hydrogen bonds : angle 4.78350 ( 2628) SS BOND : bond 0.00296 ( 41) SS BOND : angle 1.75706 ( 82) covalent geometry : bond 0.00245 (25374) covalent geometry : angle 0.48212 (34521) *********************** 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 192 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 2.585 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7278 (ptp-110) cc_final: 0.6672 (mtm110) REVERT: A 646 ARG cc_start: 0.7332 (mtm180) cc_final: 0.6958 (mtp180) REVERT: A 955 ASN cc_start: 0.7594 (m-40) cc_final: 0.7357 (m110) REVERT: A 1107 ARG cc_start: 0.7816 (mtp180) cc_final: 0.7533 (mtp180) REVERT: A 1128 VAL cc_start: 0.8377 (m) cc_final: 0.8049 (p) REVERT: B 449 TYR cc_start: 0.6406 (m-80) cc_final: 0.6119 (m-80) REVERT: B 616 ASN cc_start: 0.6518 (p0) cc_final: 0.5943 (t0) REVERT: B 904 TYR cc_start: 0.7569 (m-10) cc_final: 0.7227 (m-80) REVERT: B 935 GLN cc_start: 0.7274 (tm-30) cc_final: 0.6857 (tm-30) REVERT: C 326 ILE cc_start: 0.6012 (mt) cc_final: 0.5577 (pt) REVERT: C 356 LYS cc_start: 0.7378 (tptt) cc_final: 0.7091 (tptm) outliers start: 31 outliers final: 26 residues processed: 181 average time/residue: 0.3361 time to fit residues: 101.3782 Evaluate side-chains 183 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 104 optimal weight: 30.0000 chunk 221 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 308 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 251 optimal weight: 7.9990 chunk 187 optimal weight: 0.2980 chunk 276 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.215374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130317 restraints weight = 28674.546| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.12 r_work: 0.3273 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25445 Z= 0.134 Angle : 0.516 13.040 34693 Z= 0.265 Chirality : 0.044 0.287 4014 Planarity : 0.003 0.045 4425 Dihedral : 5.086 53.492 3972 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.07 % Allowed : 12.38 % Favored : 86.56 % 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: -0.11 (0.15), residues: 3081 helix: 2.26 (0.20), residues: 650 sheet: 0.31 (0.19), residues: 665 loop : -1.19 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS B 52 PHE 0.014 0.001 PHE C 906 TYR 0.027 0.001 TYR B 453 ARG 0.005 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 30) link_NAG-ASN : angle 2.17730 ( 90) hydrogen bonds : bond 0.04870 ( 926) hydrogen bonds : angle 4.80063 ( 2628) SS BOND : bond 0.00354 ( 41) SS BOND : angle 1.78321 ( 82) covalent geometry : bond 0.00321 (25374) covalent geometry : angle 0.49778 (34521) ********************** 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 189 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 2.898 Fit side-chains REVERT: A 237 ARG cc_start: 0.7296 (ptp-110) cc_final: 0.6470 (mtm110) REVERT: A 646 ARG cc_start: 0.7351 (mtm180) cc_final: 0.6956 (mtp180) REVERT: A 955 ASN cc_start: 0.7642 (m-40) cc_final: 0.7409 (m110) REVERT: A 1107 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7435 (mtp180) REVERT: A 1128 VAL cc_start: 0.8386 (m) cc_final: 0.8050 (p) REVERT: B 449 TYR cc_start: 0.6463 (m-80) cc_final: 0.6154 (m-80) REVERT: B 616 ASN cc_start: 0.6481 (p0) cc_final: 0.5951 (t0) REVERT: B 904 TYR cc_start: 0.7593 (m-10) cc_final: 0.7239 (m-80) REVERT: B 935 GLN cc_start: 0.7326 (tm-30) cc_final: 0.6909 (tm-30) REVERT: C 326 ILE cc_start: 0.6074 (mt) cc_final: 0.5627 (pt) REVERT: C 356 LYS cc_start: 0.7429 (tptt) cc_final: 0.7142 (tptm) outliers start: 29 outliers final: 26 residues processed: 180 average time/residue: 0.3330 time to fit residues: 99.6786 Evaluate side-chains 184 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 199 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 142 optimal weight: 0.0770 chunk 138 optimal weight: 5.9990 chunk 65 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.217695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133820 restraints weight = 28718.023| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.29 r_work: 0.3291 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25445 Z= 0.097 Angle : 0.481 13.081 34693 Z= 0.247 Chirality : 0.043 0.300 4014 Planarity : 0.003 0.043 4425 Dihedral : 4.830 54.103 3972 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.03 % Allowed : 12.34 % Favored : 86.63 % 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: 0.04 (0.15), residues: 3081 helix: 2.44 (0.20), residues: 653 sheet: 0.35 (0.19), residues: 679 loop : -1.10 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.000 HIS B 52 PHE 0.012 0.001 PHE A 592 TYR 0.027 0.001 TYR B 453 ARG 0.004 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 30) link_NAG-ASN : angle 2.09510 ( 90) hydrogen bonds : bond 0.04116 ( 926) hydrogen bonds : angle 4.64721 ( 2628) SS BOND : bond 0.00285 ( 41) SS BOND : angle 1.53009 ( 82) covalent geometry : bond 0.00219 (25374) covalent geometry : angle 0.46458 (34521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14242.33 seconds wall clock time: 243 minutes 38.87 seconds (14618.87 seconds total)