Starting phenix.real_space_refine on Mon Aug 25 03:28:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ayy_44002/08_2025/9ayy_44002_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ayy_44002/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ayy_44002/08_2025/9ayy_44002_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ayy_44002/08_2025/9ayy_44002_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ayy_44002/08_2025/9ayy_44002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ayy_44002/08_2025/9ayy_44002.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.26, per 1000 atoms: 0.25 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: 2.10 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5862 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 50 sheets defined 25.4% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 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: 6.48 Time building geometry restraints manager: 2.75 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: 0.02 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.740 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.310 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (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 ARG 0.007 0.000 ARG C 237 TYR 0.046 0.001 TYR B 453 PHE 0.030 0.002 PHE C 906 TRP 0.023 0.002 TRP B 886 HIS 0.007 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00460 (25374) covalent geometry : angle 0.73131 (34521) SS BOND : bond 0.00506 ( 41) SS BOND : angle 2.13779 ( 82) hydrogen bonds : bond 0.22499 ( 926) hydrogen bonds : angle 8.22184 ( 2628) link_NAG-ASN : bond 0.00710 ( 30) link_NAG-ASN : angle 3.00711 ( 90) *********************** 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 : 0.881 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: 0.1478 time to fit residues: 44.2378 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 : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.0670 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0010 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 overall best weight: 0.6304 ------------------------------------------------------------------------------- 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 196 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN C 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.218036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.138611 restraints weight = 28382.202| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.63 r_work: 0.3341 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25445 Z= 0.109 Angle : 0.519 13.221 34693 Z= 0.269 Chirality : 0.043 0.339 4014 Planarity : 0.004 0.052 4425 Dihedral : 5.964 57.518 3972 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.37 % Allowed : 5.41 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.15), residues: 3081 helix: 1.45 (0.20), residues: 648 sheet: 0.19 (0.20), residues: 681 loop : -1.22 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 577 TYR 0.016 0.001 TYR B1067 PHE 0.020 0.001 PHE A 592 TRP 0.011 0.001 TRP C 886 HIS 0.004 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00242 (25374) covalent geometry : angle 0.50225 (34521) SS BOND : bond 0.00297 ( 41) SS BOND : angle 1.53515 ( 82) hydrogen bonds : bond 0.04905 ( 926) hydrogen bonds : angle 5.75066 ( 2628) link_NAG-ASN : bond 0.00452 ( 30) link_NAG-ASN : angle 2.23695 ( 90) *********************** 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 170 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.7344 (tt) cc_final: 0.7121 (tt) REVERT: A 237 ARG cc_start: 0.7439 (ptp-110) cc_final: 0.6597 (ptp90) REVERT: A 955 ASN cc_start: 0.7489 (m110) cc_final: 0.7277 (m110) REVERT: B 613 GLN cc_start: 0.7991 (mt0) cc_final: 0.7700 (mt0) REVERT: B 616 ASN cc_start: 0.6791 (p0) cc_final: 0.6152 (t0) REVERT: C 355 ARG cc_start: 0.7917 (ttm110) cc_final: 0.7091 (mmm-85) REVERT: C 356 LYS cc_start: 0.7182 (tptt) cc_final: 0.6944 (tptt) REVERT: C 754 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8071 (mp) outliers start: 10 outliers final: 5 residues processed: 163 average time/residue: 0.1414 time to fit residues: 37.9863 Evaluate side-chains 146 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 325 SER 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 295 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 113 optimal weight: 0.0370 chunk 85 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 286 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.216434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.130885 restraints weight = 28460.035| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.97 r_work: 0.3325 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25445 Z= 0.123 Angle : 0.506 13.029 34693 Z= 0.262 Chirality : 0.044 0.313 4014 Planarity : 0.003 0.047 4425 Dihedral : 5.515 58.194 3972 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.59 % Allowed : 7.62 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.15), residues: 3081 helix: 1.77 (0.20), residues: 659 sheet: 0.30 (0.19), residues: 664 loop : -1.22 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1014 TYR 0.018 0.001 TYR B1067 PHE 0.018 0.001 PHE C 906 TRP 0.011 0.001 TRP B 436 HIS 0.003 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00287 (25374) covalent geometry : angle 0.48978 (34521) SS BOND : bond 0.00278 ( 41) SS BOND : angle 1.51343 ( 82) hydrogen bonds : bond 0.04884 ( 926) hydrogen bonds : angle 5.29849 ( 2628) link_NAG-ASN : bond 0.00433 ( 30) link_NAG-ASN : angle 2.16401 ( 90) *********************** 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 175 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7445 (ptp-110) cc_final: 0.6533 (ptp90) REVERT: A 646 ARG cc_start: 0.7346 (mtm180) cc_final: 0.6906 (mtp180) REVERT: A 955 ASN cc_start: 0.7464 (m110) cc_final: 0.7236 (m110) REVERT: B 206 LYS cc_start: 0.4997 (ttpp) cc_final: 0.4519 (tptm) REVERT: B 592 PHE cc_start: 0.6126 (p90) cc_final: 0.5880 (p90) REVERT: B 616 ASN cc_start: 0.6796 (p0) cc_final: 0.6253 (t0) REVERT: B 904 TYR cc_start: 0.7417 (m-10) cc_final: 0.7157 (m-80) REVERT: C 356 LYS cc_start: 0.7249 (tptt) cc_final: 0.6914 (tptm) REVERT: C 754 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8073 (mp) outliers start: 16 outliers final: 10 residues processed: 169 average time/residue: 0.1288 time to fit residues: 35.5364 Evaluate side-chains 156 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 525 CYS 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 723 THR Chi-restraints excluded: chain C residue 754 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 0.2980 chunk 216 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 295 optimal weight: 0.6980 chunk 158 optimal weight: 9.9990 chunk 304 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 955 ASN ** 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** C1101 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.215541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.130450 restraints weight = 28404.028| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.09 r_work: 0.3273 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25445 Z= 0.128 Angle : 0.505 12.872 34693 Z= 0.260 Chirality : 0.044 0.300 4014 Planarity : 0.003 0.045 4425 Dihedral : 5.192 53.780 3972 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.88 % Allowed : 8.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.15), residues: 3081 helix: 1.90 (0.20), residues: 663 sheet: 0.28 (0.19), residues: 664 loop : -1.19 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 905 TYR 0.018 0.001 TYR B1067 PHE 0.023 0.001 PHE C 906 TRP 0.012 0.001 TRP C 886 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00305 (25374) covalent geometry : angle 0.48793 (34521) SS BOND : bond 0.00298 ( 41) SS BOND : angle 1.62470 ( 82) hydrogen bonds : bond 0.04850 ( 926) hydrogen bonds : angle 5.05873 ( 2628) link_NAG-ASN : bond 0.00433 ( 30) link_NAG-ASN : angle 2.13491 ( 90) *********************** 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 185 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.6562 (tp) cc_final: 0.6342 (mp) REVERT: A 237 ARG cc_start: 0.7471 (ptp-110) cc_final: 0.6510 (mtm110) REVERT: A 646 ARG cc_start: 0.7345 (mtm180) cc_final: 0.6947 (mtp180) REVERT: A 955 ASN cc_start: 0.7654 (m-40) cc_final: 0.7376 (m110) REVERT: A 1107 ARG cc_start: 0.7926 (mtp180) cc_final: 0.7675 (mtp180) REVERT: B 49 HIS cc_start: 0.7533 (t-90) cc_final: 0.7315 (t-170) REVERT: B 592 PHE cc_start: 0.6124 (p90) cc_final: 0.5866 (p90) REVERT: B 616 ASN cc_start: 0.6805 (p0) cc_final: 0.6258 (t0) REVERT: B 904 TYR cc_start: 0.7500 (m-10) cc_final: 0.7175 (m-80) REVERT: C 356 LYS cc_start: 0.7416 (tptt) cc_final: 0.7087 (tptm) outliers start: 24 outliers final: 17 residues processed: 177 average time/residue: 0.1344 time to fit residues: 39.5714 Evaluate side-chains 172 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 900 MET 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 300 optimal weight: 0.4980 chunk 123 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 92 optimal weight: 0.0000 chunk 75 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 223 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.215541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.127559 restraints weight = 28759.795| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.12 r_work: 0.3290 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25445 Z= 0.130 Angle : 0.506 13.275 34693 Z= 0.260 Chirality : 0.044 0.308 4014 Planarity : 0.003 0.043 4425 Dihedral : 5.071 53.921 3972 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.10 % Allowed : 10.02 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.15), residues: 3081 helix: 1.95 (0.20), residues: 664 sheet: 0.28 (0.19), residues: 669 loop : -1.19 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1014 TYR 0.025 0.001 TYR B 453 PHE 0.023 0.001 PHE C 906 TRP 0.011 0.001 TRP B 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00313 (25374) covalent geometry : angle 0.48849 (34521) SS BOND : bond 0.00302 ( 41) SS BOND : angle 1.68302 ( 82) hydrogen bonds : bond 0.04847 ( 926) hydrogen bonds : angle 4.97360 ( 2628) link_NAG-ASN : bond 0.00409 ( 30) link_NAG-ASN : angle 2.18558 ( 90) *********************** 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 185 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.6607 (tp) cc_final: 0.6389 (mp) REVERT: A 237 ARG cc_start: 0.7393 (ptp-110) cc_final: 0.6731 (mtm110) REVERT: A 646 ARG cc_start: 0.7338 (mtm180) cc_final: 0.6960 (mtp180) REVERT: A 814 LYS cc_start: 0.8408 (mmtm) cc_final: 0.7357 (ptmm) REVERT: A 955 ASN cc_start: 0.7657 (m-40) cc_final: 0.7392 (m110) REVERT: A 1107 ARG cc_start: 0.7846 (mtp180) cc_final: 0.7622 (mtp180) REVERT: B 49 HIS cc_start: 0.7623 (t-90) cc_final: 0.7381 (t-170) REVERT: B 616 ASN cc_start: 0.6515 (p0) cc_final: 0.5776 (t0) REVERT: B 904 TYR cc_start: 0.7509 (m-10) cc_final: 0.7202 (m-80) REVERT: C 356 LYS cc_start: 0.7281 (tptt) cc_final: 0.6968 (tptm) outliers start: 30 outliers final: 22 residues processed: 175 average time/residue: 0.1357 time to fit residues: 39.5724 Evaluate side-chains 171 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 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 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 126 VAL 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 89 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 282 optimal weight: 0.0470 chunk 269 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 297 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.216660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130265 restraints weight = 28756.492| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.09 r_work: 0.3299 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25445 Z= 0.102 Angle : 0.482 13.267 34693 Z= 0.247 Chirality : 0.043 0.306 4014 Planarity : 0.003 0.042 4425 Dihedral : 4.888 54.070 3972 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.25 % Allowed : 10.57 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.15), residues: 3081 helix: 2.07 (0.20), residues: 666 sheet: 0.33 (0.19), residues: 673 loop : -1.14 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 357 TYR 0.025 0.001 TYR B 453 PHE 0.012 0.001 PHE A 592 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.000 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00233 (25374) covalent geometry : angle 0.46446 (34521) SS BOND : bond 0.00326 ( 41) SS BOND : angle 1.55144 ( 82) hydrogen bonds : bond 0.04403 ( 926) hydrogen bonds : angle 4.83291 ( 2628) link_NAG-ASN : bond 0.00422 ( 30) link_NAG-ASN : angle 2.11751 ( 90) *********************** 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 189 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.6584 (tp) cc_final: 0.6373 (mp) REVERT: A 237 ARG cc_start: 0.7380 (ptp-110) cc_final: 0.6703 (mtm110) REVERT: A 646 ARG cc_start: 0.7351 (mtm180) cc_final: 0.6954 (mtp180) REVERT: A 814 LYS cc_start: 0.8395 (mmtm) cc_final: 0.7346 (ptmm) REVERT: A 955 ASN cc_start: 0.7629 (m-40) cc_final: 0.7350 (m110) REVERT: A 1107 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7581 (mtp180) REVERT: B 49 HIS cc_start: 0.7620 (t-90) cc_final: 0.7368 (t-170) REVERT: B 616 ASN cc_start: 0.6462 (p0) cc_final: 0.5830 (t0) REVERT: B 904 TYR cc_start: 0.7565 (m-10) cc_final: 0.7250 (m-80) REVERT: C 356 LYS cc_start: 0.7233 (tptt) cc_final: 0.6929 (tptm) REVERT: C 740 MET cc_start: 0.8760 (ttt) cc_final: 0.8416 (ttm) REVERT: C 977 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7746 (mp) outliers start: 34 outliers final: 27 residues processed: 178 average time/residue: 0.1286 time to fit residues: 38.1058 Evaluate side-chains 180 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 900 MET 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 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 314 GLN Chi-restraints excluded: chain C residue 358 ILE 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 977 LEU Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 21 optimal weight: 0.5980 chunk 134 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 167 optimal weight: 1.9990 chunk 300 optimal weight: 0.8980 chunk 220 optimal weight: 8.9990 chunk 188 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 chunk 251 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.216463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131847 restraints weight = 28327.645| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.88 r_work: 0.3321 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25445 Z= 0.096 Angle : 0.469 13.167 34693 Z= 0.240 Chirality : 0.043 0.303 4014 Planarity : 0.003 0.042 4425 Dihedral : 4.680 53.842 3972 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.07 % Allowed : 11.16 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.15), residues: 3081 helix: 2.27 (0.20), residues: 670 sheet: 0.41 (0.19), residues: 671 loop : -1.09 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 567 TYR 0.024 0.001 TYR B 453 PHE 0.014 0.001 PHE B 592 TRP 0.009 0.001 TRP B 436 HIS 0.002 0.000 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00218 (25374) covalent geometry : angle 0.45286 (34521) SS BOND : bond 0.00269 ( 41) SS BOND : angle 1.43440 ( 82) hydrogen bonds : bond 0.04112 ( 926) hydrogen bonds : angle 4.68367 ( 2628) link_NAG-ASN : bond 0.00422 ( 30) link_NAG-ASN : angle 2.07498 ( 90) *********************** 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 191 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.6601 (tp) cc_final: 0.6337 (mp) REVERT: A 237 ARG cc_start: 0.7374 (ptp-110) cc_final: 0.6677 (mtm110) REVERT: A 646 ARG cc_start: 0.7359 (mtm180) cc_final: 0.6936 (mtp180) REVERT: A 814 LYS cc_start: 0.8395 (mmtm) cc_final: 0.7318 (ptmm) REVERT: A 955 ASN cc_start: 0.7615 (m-40) cc_final: 0.7329 (m110) REVERT: A 1107 ARG cc_start: 0.7801 (mtp180) cc_final: 0.7534 (mtp180) REVERT: B 49 HIS cc_start: 0.7608 (t-90) cc_final: 0.7356 (t-170) REVERT: B 616 ASN cc_start: 0.6452 (p0) cc_final: 0.5889 (t0) REVERT: B 904 TYR cc_start: 0.7569 (m-10) cc_final: 0.7237 (m-80) REVERT: C 326 ILE cc_start: 0.6057 (mt) cc_final: 0.5699 (pt) REVERT: C 356 LYS cc_start: 0.7348 (tptt) cc_final: 0.7050 (tptm) REVERT: C 661 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8267 (tt0) REVERT: C 740 MET cc_start: 0.8703 (ttt) cc_final: 0.8370 (ttm) REVERT: C 977 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7771 (mp) outliers start: 29 outliers final: 21 residues processed: 180 average time/residue: 0.1378 time to fit residues: 40.7235 Evaluate side-chains 179 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 1092 GLU Chi-restraints excluded: chain B residue 291 CYS 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 1128 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 358 ILE 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 977 LEU Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 234 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 285 optimal weight: 0.9980 chunk 49 optimal weight: 0.0270 chunk 123 optimal weight: 10.0000 chunk 137 optimal weight: 0.0870 chunk 263 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 191 optimal weight: 0.9980 overall best weight: 0.8218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.216865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130965 restraints weight = 28708.341| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.28 r_work: 0.3292 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25445 Z= 0.106 Angle : 0.478 13.124 34693 Z= 0.245 Chirality : 0.043 0.294 4014 Planarity : 0.003 0.042 4425 Dihedral : 4.684 53.823 3972 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.10 % Allowed : 11.57 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.15), residues: 3081 helix: 2.21 (0.20), residues: 669 sheet: 0.42 (0.19), residues: 671 loop : -1.07 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 567 TYR 0.027 0.001 TYR B 453 PHE 0.013 0.001 PHE B 592 TRP 0.008 0.001 TRP B 436 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00247 (25374) covalent geometry : angle 0.46204 (34521) SS BOND : bond 0.00284 ( 41) SS BOND : angle 1.48666 ( 82) hydrogen bonds : bond 0.04288 ( 926) hydrogen bonds : angle 4.67812 ( 2628) link_NAG-ASN : bond 0.00417 ( 30) link_NAG-ASN : angle 2.07950 ( 90) *********************** 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 190 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.895 Fit side-chains REVERT: A 118 LEU cc_start: 0.6511 (tp) cc_final: 0.6258 (mp) REVERT: A 237 ARG cc_start: 0.7343 (ptp-110) cc_final: 0.6671 (mtm110) REVERT: A 646 ARG cc_start: 0.7406 (mtm180) cc_final: 0.6949 (mtp180) REVERT: A 814 LYS cc_start: 0.8444 (mmtm) cc_final: 0.7334 (ptmm) REVERT: A 955 ASN cc_start: 0.7717 (m-40) cc_final: 0.7427 (m110) REVERT: A 1107 ARG cc_start: 0.7849 (mtp180) cc_final: 0.7535 (mtp180) REVERT: B 49 HIS cc_start: 0.7572 (t-90) cc_final: 0.7324 (t-170) REVERT: B 616 ASN cc_start: 0.6415 (p0) cc_final: 0.5830 (t0) REVERT: B 904 TYR cc_start: 0.7607 (m-10) cc_final: 0.7261 (m-80) REVERT: B 935 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6834 (tm-30) REVERT: C 326 ILE cc_start: 0.6016 (mt) cc_final: 0.5676 (pt) REVERT: C 356 LYS cc_start: 0.7321 (tptt) cc_final: 0.7019 (tptm) REVERT: C 661 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8280 (tt0) REVERT: C 740 MET cc_start: 0.8804 (ttt) cc_final: 0.8464 (ttm) REVERT: C 977 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7729 (mp) outliers start: 30 outliers final: 26 residues processed: 181 average time/residue: 0.1474 time to fit residues: 43.9529 Evaluate side-chains 184 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 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 1128 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 238 PHE 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 723 THR Chi-restraints excluded: chain C residue 745 ASP 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 1114 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 285 optimal weight: 3.9990 chunk 293 optimal weight: 0.7980 chunk 310 optimal weight: 0.5980 chunk 131 optimal weight: 8.9990 chunk 76 optimal weight: 0.5980 chunk 277 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 275 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.216983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127918 restraints weight = 28771.797| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.60 r_work: 0.3358 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1882 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= 0.104 Angle : 0.480 13.102 34693 Z= 0.246 Chirality : 0.043 0.293 4014 Planarity : 0.003 0.042 4425 Dihedral : 4.704 53.852 3972 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.07 % Allowed : 11.75 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.15), residues: 3081 helix: 2.20 (0.20), residues: 675 sheet: 0.47 (0.19), residues: 669 loop : -1.06 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.027 0.001 TYR B 453 PHE 0.013 0.001 PHE B 592 TRP 0.008 0.001 TRP B 436 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00242 (25374) covalent geometry : angle 0.46325 (34521) SS BOND : bond 0.00273 ( 41) SS BOND : angle 1.59082 ( 82) hydrogen bonds : bond 0.04243 ( 926) hydrogen bonds : angle 4.66693 ( 2628) link_NAG-ASN : bond 0.00426 ( 30) link_NAG-ASN : angle 2.06797 ( 90) *********************** 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 186 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.842 Fit side-chains REVERT: A 118 LEU cc_start: 0.6617 (tp) cc_final: 0.6239 (mm) REVERT: A 237 ARG cc_start: 0.7411 (ptp-110) cc_final: 0.6722 (mtm110) REVERT: A 646 ARG cc_start: 0.7476 (mtm180) cc_final: 0.6935 (mtp180) REVERT: A 814 LYS cc_start: 0.8514 (mmtm) cc_final: 0.7307 (ptmm) REVERT: A 1107 ARG cc_start: 0.8092 (mtp180) cc_final: 0.7711 (mtp180) REVERT: B 49 HIS cc_start: 0.7608 (t-90) cc_final: 0.7361 (t-170) REVERT: B 616 ASN cc_start: 0.6415 (p0) cc_final: 0.5772 (t0) REVERT: B 904 TYR cc_start: 0.7748 (m-10) cc_final: 0.7372 (m-80) REVERT: B 935 GLN cc_start: 0.7147 (tm-30) cc_final: 0.6743 (tm-30) REVERT: C 326 ILE cc_start: 0.6017 (mt) cc_final: 0.5690 (pt) REVERT: C 356 LYS cc_start: 0.7379 (tptt) cc_final: 0.7080 (tptm) REVERT: C 661 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8395 (tt0) REVERT: C 740 MET cc_start: 0.8629 (ttt) cc_final: 0.8312 (ttm) REVERT: C 977 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7766 (mp) outliers start: 29 outliers final: 26 residues processed: 176 average time/residue: 0.1465 time to fit residues: 42.5214 Evaluate side-chains 183 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 1092 GLU Chi-restraints excluded: chain B residue 291 CYS 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 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 745 ASP 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 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 104 optimal weight: 30.0000 chunk 90 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 284 optimal weight: 0.8980 chunk 298 optimal weight: 0.8980 chunk 246 optimal weight: 0.8980 chunk 139 optimal weight: 0.1980 chunk 250 optimal weight: 0.0980 chunk 126 optimal weight: 0.9980 chunk 143 optimal weight: 20.0000 chunk 120 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.217201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.133443 restraints weight = 28254.183| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.92 r_work: 0.3321 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25445 Z= 0.096 Angle : 0.472 13.124 34693 Z= 0.242 Chirality : 0.043 0.295 4014 Planarity : 0.003 0.042 4425 Dihedral : 4.645 53.851 3972 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.10 % Allowed : 11.71 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.15), residues: 3081 helix: 2.26 (0.20), residues: 675 sheet: 0.52 (0.19), residues: 667 loop : -1.02 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.028 0.001 TYR B 453 PHE 0.012 0.001 PHE A 592 TRP 0.008 0.001 TRP B 436 HIS 0.002 0.000 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00219 (25374) covalent geometry : angle 0.45582 (34521) SS BOND : bond 0.00270 ( 41) SS BOND : angle 1.49884 ( 82) hydrogen bonds : bond 0.04068 ( 926) hydrogen bonds : angle 4.61230 ( 2628) link_NAG-ASN : bond 0.00428 ( 30) link_NAG-ASN : angle 2.05241 ( 90) ********************** 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 190 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.863 Fit side-chains REVERT: A 118 LEU cc_start: 0.6522 (tp) cc_final: 0.6161 (mm) REVERT: A 237 ARG cc_start: 0.7334 (ptp-110) cc_final: 0.6673 (mtm110) REVERT: A 646 ARG cc_start: 0.7355 (mtm180) cc_final: 0.6957 (mtp180) REVERT: A 814 LYS cc_start: 0.8411 (mmtm) cc_final: 0.7318 (ptmm) REVERT: A 955 ASN cc_start: 0.7654 (m-40) cc_final: 0.7414 (m110) REVERT: A 1107 ARG cc_start: 0.7752 (mtp180) cc_final: 0.7427 (mtp180) REVERT: B 49 HIS cc_start: 0.7576 (t-90) cc_final: 0.7335 (t-170) REVERT: B 616 ASN cc_start: 0.6423 (p0) cc_final: 0.5890 (t0) REVERT: B 904 TYR cc_start: 0.7556 (m-10) cc_final: 0.7258 (m-80) REVERT: B 935 GLN cc_start: 0.7175 (tm-30) cc_final: 0.6784 (tm-30) REVERT: C 326 ILE cc_start: 0.6045 (mt) cc_final: 0.5714 (pt) REVERT: C 356 LYS cc_start: 0.7501 (tptt) cc_final: 0.7196 (tptm) REVERT: C 661 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8239 (tt0) REVERT: C 740 MET cc_start: 0.8500 (ttt) cc_final: 0.8173 (ttm) REVERT: C 977 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7799 (mp) outliers start: 30 outliers final: 27 residues processed: 180 average time/residue: 0.1495 time to fit residues: 44.5030 Evaluate side-chains 184 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 1128 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 358 ILE 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 1125 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 90 optimal weight: 0.5980 chunk 230 optimal weight: 2.9990 chunk 262 optimal weight: 7.9990 chunk 189 optimal weight: 0.7980 chunk 249 optimal weight: 0.0570 chunk 190 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 295 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 804 GLN B 422 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.216789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131778 restraints weight = 28617.313| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.23 r_work: 0.3276 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25445 Z= 0.126 Angle : 0.500 13.053 34693 Z= 0.256 Chirality : 0.044 0.283 4014 Planarity : 0.003 0.040 4425 Dihedral : 4.788 53.551 3972 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.10 % Allowed : 11.86 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.15), residues: 3081 helix: 2.40 (0.20), residues: 650 sheet: 0.48 (0.19), residues: 671 loop : -1.05 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.027 0.001 TYR B 453 PHE 0.015 0.001 PHE C 906 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00300 (25374) covalent geometry : angle 0.48216 (34521) SS BOND : bond 0.00322 ( 41) SS BOND : angle 1.68675 ( 82) hydrogen bonds : bond 0.04628 ( 926) hydrogen bonds : angle 4.68175 ( 2628) link_NAG-ASN : bond 0.00424 ( 30) link_NAG-ASN : angle 2.10417 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6542.89 seconds wall clock time: 112 minutes 26.22 seconds (6746.22 seconds total)