Starting phenix.real_space_refine on Sat Jun 21 13:18:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ayw_44000/06_2025/9ayw_44000_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ayw_44000/06_2025/9ayw_44000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ayw_44000/06_2025/9ayw_44000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ayw_44000/06_2025/9ayw_44000.map" model { file = "/net/cci-nas-00/data/ceres_data/9ayw_44000/06_2025/9ayw_44000_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ayw_44000/06_2025/9ayw_44000_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.069 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 39 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24813 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8131 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "B" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8131 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "C" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8131 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 15.51, per 1000 atoms: 0.63 Number of scatterers: 24813 At special positions: 0 Unit cell: (137.16, 128.52, 173.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 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=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.06 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=2.04 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=2.03 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: 5.47 Conformation dependent library (CDL) restraints added in 3.6 seconds 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5862 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 47 sheets defined 25.6% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.508A pdb=" N ASN A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 4.177A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.883A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) 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 782 removed outlier: 3.600A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.581A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.665A 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 945 through 965 removed outlier: 3.785A 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: 3.568A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.545A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.828A 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 338 through 343 removed outlier: 4.232A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.904A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.595A 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: 4.025A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.268A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.840A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (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: 3.576A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.516A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 842 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 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.539A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.566A 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: 3.546A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.713A 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: 3.504A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.531A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.837A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.658A pdb=" N ASN C 343 " --> pdb=" O HIS C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.842A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 368' Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.538A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 387' Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.674A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 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: 3.576A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 842 Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.568A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.517A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.513A 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: 3.617A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.635A 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 1033 removed outlier: 3.509A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.984A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.846A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.477A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.986A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.153A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.557A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.402A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.617A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.704A pdb=" N ALA A 435 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA A 376 " --> pdb=" O ALA A 435 " (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 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.067A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.830A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.700A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.168A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.567A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.989A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.002A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.705A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.585A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 318 removed outlier: 7.044A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.746A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.691A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.955A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.714A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.948A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.559A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 25 through 30 removed outlier: 7.785A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.040A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.533A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.030A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.541A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.568A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.638A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.101A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.808A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.138A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.591A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 1019 hydrogen bonds defined for protein. 2799 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.74 Time building geometry restraints manager: 6.65 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: 7933 1.35 - 1.48: 6653 1.48 - 1.62: 10647 1.62 - 1.75: 0 1.75 - 1.88: 141 Bond restraints: 25374 Sorted by residual: bond pdb=" C ALA C1056 " pdb=" N PRO C1057 " ideal model delta sigma weight residual 1.332 1.359 -0.027 1.12e-02 7.97e+03 5.79e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " ideal model delta sigma weight residual 1.808 1.881 -0.073 3.30e-02 9.18e+02 4.93e+00 bond pdb=" C LEU B 560 " pdb=" N PRO B 561 " ideal model delta sigma weight residual 1.337 1.358 -0.022 9.80e-03 1.04e+04 4.81e+00 bond pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.81e+00 ... (remaining 25369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 34318 3.48 - 6.96: 176 6.96 - 10.44: 23 10.44 - 13.92: 1 13.92 - 17.40: 3 Bond angle restraints: 34521 Sorted by residual: angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 131.80 -17.40 2.30e+00 1.89e-01 5.72e+01 angle pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " ideal model delta sigma weight residual 114.40 129.85 -15.45 2.30e+00 1.89e-01 4.52e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 128.73 -14.33 2.30e+00 1.89e-01 3.88e+01 angle pdb=" CA CYS C 649 " pdb=" CB CYS C 649 " pdb=" SG CYS C 649 " ideal model delta sigma weight residual 114.40 123.95 -9.55 2.30e+00 1.89e-01 1.72e+01 angle pdb=" CA CYS B 391 " pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 114.40 123.89 -9.49 2.30e+00 1.89e-01 1.70e+01 ... (remaining 34516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 14038 18.02 - 36.03: 1229 36.03 - 54.05: 187 54.05 - 72.07: 54 72.07 - 90.09: 35 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 93.00 -176.91 -90.09 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -167.38 81.38 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 165.31 -72.31 1 1.00e+01 1.00e-02 6.68e+01 ... (remaining 15540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 3987 0.177 - 0.355: 26 0.355 - 0.532: 0 0.532 - 0.709: 0 0.709 - 0.887: 1 Chirality restraints: 4014 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" CG LEU A 390 " pdb=" CB LEU A 390 " pdb=" CD1 LEU A 390 " pdb=" CD2 LEU A 390 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CG LEU A 916 " pdb=" CB LEU A 916 " pdb=" CD1 LEU A 916 " pdb=" CD2 LEU A 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 4011 not shown) Planarity restraints: 4455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.005 2.00e-02 2.50e+03 3.69e-02 1.70e+01 pdb=" CG ASN A 343 " 0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.034 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 138 " -0.058 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO C 139 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 139 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 139 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " -0.020 2.00e-02 2.50e+03 1.87e-02 6.10e+00 pdb=" CG PHE A 906 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.005 2.00e-02 2.50e+03 ... (remaining 4452 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6696 2.81 - 3.33: 19638 3.33 - 3.86: 39869 3.86 - 4.38: 45735 4.38 - 4.90: 82132 Nonbonded interactions: 194070 Sorted by model distance: nonbonded pdb=" OE2 GLU B 298 " pdb=" OG SER B 316 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.313 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.317 3.040 ... (remaining 194065 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: 0.08 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 59.080 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 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 0.073 25445 Z= 0.222 Angle : 0.804 17.401 34693 Z= 0.420 Chirality : 0.057 0.887 4014 Planarity : 0.006 0.089 4425 Dihedral : 14.170 89.980 9558 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % 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 : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3081 helix: 0.13 (0.18), residues: 627 sheet: 0.79 (0.18), residues: 762 loop : -1.43 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 886 HIS 0.008 0.001 HIS A 339 PHE 0.043 0.002 PHE A 906 TYR 0.036 0.002 TYR C 453 ARG 0.016 0.001 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 30) link_NAG-ASN : angle 2.59361 ( 90) hydrogen bonds : bond 0.13918 ( 1013) hydrogen bonds : angle 6.18015 ( 2799) SS BOND : bond 0.00719 ( 41) SS BOND : angle 2.69495 ( 82) covalent geometry : bond 0.00485 (25374) covalent geometry : angle 0.78371 (34521) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 SER cc_start: 0.8794 (p) cc_final: 0.8204 (m) REVERT: B 731 MET cc_start: 0.8910 (ptt) cc_final: 0.8491 (ptt) REVERT: B 851 CYS cc_start: 0.7552 (m) cc_final: 0.7148 (m) REVERT: C 220 PHE cc_start: 0.8144 (m-80) cc_final: 0.7886 (m-80) REVERT: C 995 ARG cc_start: 0.7662 (mtt-85) cc_final: 0.7408 (mtm180) outliers start: 0 outliers final: 1 residues processed: 286 average time/residue: 1.1479 time to fit residues: 388.5523 Evaluate side-chains 202 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 159 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 564 GLN A 710 ASN A 804 GLN B 321 GLN B 334 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B1010 GLN B1088 HIS C 448 ASN C 493 GLN C 606 ASN C 762 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.171507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.129098 restraints weight = 26652.272| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.76 r_work: 0.3141 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25445 Z= 0.148 Angle : 0.565 10.343 34693 Z= 0.293 Chirality : 0.045 0.222 4014 Planarity : 0.004 0.062 4425 Dihedral : 6.321 57.032 3974 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.22 % Allowed : 7.92 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 3081 helix: 1.62 (0.20), residues: 645 sheet: 0.95 (0.18), residues: 798 loop : -1.25 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS A 207 PHE 0.024 0.002 PHE A 906 TYR 0.017 0.001 TYR C1067 ARG 0.008 0.000 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 30) link_NAG-ASN : angle 1.79946 ( 90) hydrogen bonds : bond 0.05232 ( 1013) hydrogen bonds : angle 4.79176 ( 2799) SS BOND : bond 0.00404 ( 41) SS BOND : angle 2.30074 ( 82) covalent geometry : bond 0.00355 (25374) covalent geometry : angle 0.54709 (34521) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 592 PHE cc_start: 0.7743 (p90) cc_final: 0.7529 (p90) REVERT: B 731 MET cc_start: 0.9128 (ptt) cc_final: 0.8772 (ptt) REVERT: B 851 CYS cc_start: 0.8386 (m) cc_final: 0.8122 (m) REVERT: C 776 LYS cc_start: 0.8181 (tttp) cc_final: 0.7954 (tttt) outliers start: 33 outliers final: 16 residues processed: 241 average time/residue: 1.0833 time to fit residues: 313.6053 Evaluate side-chains 217 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 723 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 308 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 276 optimal weight: 0.2980 chunk 304 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 303 optimal weight: 1.9990 chunk 279 optimal weight: 0.7980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN B 30 ASN B 339 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.169589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.127808 restraints weight = 26523.364| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.52 r_work: 0.3095 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25445 Z= 0.157 Angle : 0.567 11.186 34693 Z= 0.293 Chirality : 0.045 0.202 4014 Planarity : 0.004 0.048 4425 Dihedral : 5.857 53.755 3972 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.80 % Allowed : 10.76 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3081 helix: 2.09 (0.21), residues: 648 sheet: 0.83 (0.18), residues: 756 loop : -1.15 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS B1058 PHE 0.026 0.002 PHE A 906 TYR 0.018 0.001 TYR C1067 ARG 0.008 0.000 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 30) link_NAG-ASN : angle 1.87614 ( 90) hydrogen bonds : bond 0.05315 ( 1013) hydrogen bonds : angle 4.68255 ( 2799) SS BOND : bond 0.00438 ( 41) SS BOND : angle 2.36771 ( 82) covalent geometry : bond 0.00383 (25374) covalent geometry : angle 0.54850 (34521) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.8433 (m-10) cc_final: 0.8067 (m-80) REVERT: A 443 SER cc_start: 0.8251 (m) cc_final: 0.7955 (p) REVERT: A 904 TYR cc_start: 0.7814 (m-10) cc_final: 0.7579 (m-10) REVERT: B 291 CYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7008 (m) REVERT: B 498 ARG cc_start: 0.7903 (mtt-85) cc_final: 0.7696 (mtt90) REVERT: B 731 MET cc_start: 0.9209 (ptt) cc_final: 0.8832 (ptt) REVERT: C 33 THR cc_start: 0.8554 (t) cc_final: 0.8175 (m) REVERT: C 776 LYS cc_start: 0.8231 (tttp) cc_final: 0.8022 (tttt) outliers start: 49 outliers final: 33 residues processed: 247 average time/residue: 1.1129 time to fit residues: 330.0462 Evaluate side-chains 235 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 214 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 188 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 240 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 564 GLN B 321 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 218 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.169370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126816 restraints weight = 26787.463| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.69 r_work: 0.3107 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25445 Z= 0.146 Angle : 0.548 11.508 34693 Z= 0.283 Chirality : 0.045 0.205 4014 Planarity : 0.004 0.049 4425 Dihedral : 5.436 53.867 3972 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.47 % Allowed : 12.34 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3081 helix: 2.07 (0.20), residues: 669 sheet: 0.68 (0.18), residues: 777 loop : -1.11 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS C 69 PHE 0.022 0.001 PHE A 906 TYR 0.017 0.001 TYR C1067 ARG 0.009 0.000 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 30) link_NAG-ASN : angle 1.91589 ( 90) hydrogen bonds : bond 0.05054 ( 1013) hydrogen bonds : angle 4.58236 ( 2799) SS BOND : bond 0.00474 ( 41) SS BOND : angle 2.23395 ( 82) covalent geometry : bond 0.00355 (25374) covalent geometry : angle 0.52987 (34521) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 226 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8077 (m) REVERT: A 281 GLU cc_start: 0.8190 (pm20) cc_final: 0.7809 (pm20) REVERT: A 443 SER cc_start: 0.8309 (m) cc_final: 0.7992 (p) REVERT: A 904 TYR cc_start: 0.7623 (m-10) cc_final: 0.7420 (m-10) REVERT: B 731 MET cc_start: 0.9167 (ptt) cc_final: 0.8768 (ptt) REVERT: C 33 THR cc_start: 0.8492 (t) cc_final: 0.8116 (m) REVERT: C 271 GLN cc_start: 0.8518 (mt0) cc_final: 0.8295 (mt0) REVERT: C 531 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7739 (p) REVERT: C 776 LYS cc_start: 0.8114 (tttp) cc_final: 0.7898 (tttt) outliers start: 67 outliers final: 43 residues processed: 265 average time/residue: 1.0015 time to fit residues: 321.0767 Evaluate side-chains 251 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 2.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 242 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A1101 HIS B 49 HIS ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1010 GLN C 69 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.165356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123053 restraints weight = 26843.779| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.61 r_work: 0.3103 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 25445 Z= 0.251 Angle : 0.662 13.051 34693 Z= 0.340 Chirality : 0.049 0.234 4014 Planarity : 0.004 0.049 4425 Dihedral : 5.768 52.261 3972 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.50 % Allowed : 13.48 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 3081 helix: 1.66 (0.20), residues: 687 sheet: 0.63 (0.18), residues: 765 loop : -1.19 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 436 HIS 0.006 0.001 HIS A 207 PHE 0.029 0.002 PHE A 906 TYR 0.019 0.002 TYR C1067 ARG 0.008 0.001 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 30) link_NAG-ASN : angle 2.33511 ( 90) hydrogen bonds : bond 0.06431 ( 1013) hydrogen bonds : angle 4.83736 ( 2799) SS BOND : bond 0.00526 ( 41) SS BOND : angle 2.81927 ( 82) covalent geometry : bond 0.00629 (25374) covalent geometry : angle 0.63806 (34521) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 224 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7649 (t80) REVERT: A 281 GLU cc_start: 0.8305 (pm20) cc_final: 0.7997 (pm20) REVERT: A 346 THR cc_start: 0.8249 (p) cc_final: 0.7956 (t) REVERT: A 443 SER cc_start: 0.8245 (m) cc_final: 0.7958 (p) REVERT: B 191 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6896 (mm-30) REVERT: B 319 ARG cc_start: 0.7619 (mmm-85) cc_final: 0.7352 (mmt90) REVERT: B 731 MET cc_start: 0.9232 (ptt) cc_final: 0.8919 (ptt) REVERT: B 995 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7478 (mtt-85) REVERT: C 33 THR cc_start: 0.8641 (t) cc_final: 0.8341 (m) outliers start: 95 outliers final: 63 residues processed: 285 average time/residue: 1.0610 time to fit residues: 369.1132 Evaluate side-chains 266 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 201 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 202 optimal weight: 0.7980 chunk 190 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 263 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A1101 HIS B 321 GLN B 644 GLN B1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.166949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125091 restraints weight = 26606.663| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.46 r_work: 0.3127 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25445 Z= 0.161 Angle : 0.577 12.016 34693 Z= 0.297 Chirality : 0.046 0.218 4014 Planarity : 0.004 0.046 4425 Dihedral : 5.439 53.915 3972 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.20 % Allowed : 14.77 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3081 helix: 1.91 (0.20), residues: 684 sheet: 0.63 (0.17), residues: 816 loop : -1.18 (0.14), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS A 207 PHE 0.022 0.002 PHE A 318 TYR 0.016 0.001 TYR C1067 ARG 0.008 0.000 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 30) link_NAG-ASN : angle 2.06592 ( 90) hydrogen bonds : bond 0.05334 ( 1013) hydrogen bonds : angle 4.65974 ( 2799) SS BOND : bond 0.00459 ( 41) SS BOND : angle 2.45001 ( 82) covalent geometry : bond 0.00394 (25374) covalent geometry : angle 0.55571 (34521) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 211 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8151 (m) REVERT: A 238 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7713 (t80) REVERT: A 281 GLU cc_start: 0.8334 (pm20) cc_final: 0.8019 (pm20) REVERT: A 346 THR cc_start: 0.8269 (p) cc_final: 0.7975 (t) REVERT: A 443 SER cc_start: 0.8226 (m) cc_final: 0.7931 (p) REVERT: B 191 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6815 (mm-30) REVERT: B 343 ASN cc_start: 0.7595 (m110) cc_final: 0.7224 (p0) REVERT: B 731 MET cc_start: 0.9281 (ptt) cc_final: 0.8987 (ptt) REVERT: C 33 THR cc_start: 0.8601 (t) cc_final: 0.8311 (m) REVERT: C 177 MET cc_start: 0.6194 (ppp) cc_final: 0.5887 (tmt) REVERT: C 271 GLN cc_start: 0.8625 (mt0) cc_final: 0.8423 (mt0) REVERT: C 531 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7687 (p) outliers start: 87 outliers final: 63 residues processed: 271 average time/residue: 0.9645 time to fit residues: 318.4254 Evaluate side-chains 268 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 201 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 138 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 292 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A1101 HIS B 644 GLN C 69 HIS C 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.167910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125956 restraints weight = 26776.176| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.55 r_work: 0.3144 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25445 Z= 0.146 Angle : 0.561 11.496 34693 Z= 0.289 Chirality : 0.045 0.216 4014 Planarity : 0.004 0.052 4425 Dihedral : 5.327 53.734 3972 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.54 % Allowed : 14.84 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3081 helix: 2.05 (0.20), residues: 684 sheet: 0.68 (0.17), residues: 810 loop : -1.16 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS C 69 PHE 0.019 0.001 PHE A 318 TYR 0.016 0.001 TYR C1067 ARG 0.009 0.000 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 30) link_NAG-ASN : angle 1.93986 ( 90) hydrogen bonds : bond 0.05068 ( 1013) hydrogen bonds : angle 4.59630 ( 2799) SS BOND : bond 0.00445 ( 41) SS BOND : angle 2.49839 ( 82) covalent geometry : bond 0.00358 (25374) covalent geometry : angle 0.54055 (34521) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 217 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8162 (m) REVERT: A 281 GLU cc_start: 0.8334 (pm20) cc_final: 0.8032 (pm20) REVERT: A 346 THR cc_start: 0.8247 (p) cc_final: 0.7956 (t) REVERT: A 443 SER cc_start: 0.8220 (m) cc_final: 0.7918 (p) REVERT: A 532 ASN cc_start: 0.8362 (m-40) cc_final: 0.8124 (m110) REVERT: A 904 TYR cc_start: 0.7843 (m-10) cc_final: 0.7589 (m-10) REVERT: B 731 MET cc_start: 0.9273 (ptt) cc_final: 0.8975 (ptt) REVERT: C 33 THR cc_start: 0.8591 (t) cc_final: 0.8271 (m) REVERT: C 177 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.5764 (tmm) REVERT: C 271 GLN cc_start: 0.8673 (mt0) cc_final: 0.8467 (mt0) REVERT: C 531 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7709 (p) REVERT: C 904 TYR cc_start: 0.8078 (m-10) cc_final: 0.6695 (m-80) outliers start: 96 outliers final: 67 residues processed: 280 average time/residue: 0.9261 time to fit residues: 317.2748 Evaluate side-chains 277 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 207 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 166 optimal weight: 0.9990 chunk 44 optimal weight: 0.0020 chunk 49 optimal weight: 7.9990 chunk 304 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 213 optimal weight: 0.9990 chunk 262 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A1101 HIS B 30 ASN B 360 ASN B 901 GLN C 207 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.167818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125903 restraints weight = 26658.984| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.53 r_work: 0.3132 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25445 Z= 0.111 Angle : 0.537 16.401 34693 Z= 0.273 Chirality : 0.044 0.258 4014 Planarity : 0.003 0.055 4425 Dihedral : 5.349 59.958 3972 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.62 % Allowed : 15.91 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3081 helix: 2.27 (0.20), residues: 684 sheet: 0.77 (0.18), residues: 807 loop : -1.09 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS C 69 PHE 0.018 0.001 PHE A 318 TYR 0.015 0.001 TYR C1067 ARG 0.009 0.000 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 30) link_NAG-ASN : angle 2.47003 ( 90) hydrogen bonds : bond 0.04385 ( 1013) hydrogen bonds : angle 4.44787 ( 2799) SS BOND : bond 0.00434 ( 41) SS BOND : angle 2.18727 ( 82) covalent geometry : bond 0.00261 (25374) covalent geometry : angle 0.51221 (34521) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 216 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8213 (m-80) cc_final: 0.7811 (m-80) REVERT: A 281 GLU cc_start: 0.8211 (pm20) cc_final: 0.7912 (pm20) REVERT: A 443 SER cc_start: 0.8165 (m) cc_final: 0.7857 (p) REVERT: A 904 TYR cc_start: 0.7636 (m-10) cc_final: 0.7406 (m-10) REVERT: B 191 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6617 (mm-30) REVERT: B 731 MET cc_start: 0.9208 (ptt) cc_final: 0.8781 (ptt) REVERT: B 1139 ASP cc_start: 0.8083 (t0) cc_final: 0.7783 (t70) REVERT: C 33 THR cc_start: 0.8463 (t) cc_final: 0.8138 (m) REVERT: C 177 MET cc_start: 0.6335 (OUTLIER) cc_final: 0.5761 (tmm) REVERT: C 531 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7732 (p) REVERT: C 904 TYR cc_start: 0.7877 (m-10) cc_final: 0.6442 (m-80) outliers start: 71 outliers final: 50 residues processed: 266 average time/residue: 1.0045 time to fit residues: 328.0293 Evaluate side-chains 257 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 204 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 112 optimal weight: 9.9990 chunk 307 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 264 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 278 optimal weight: 0.9980 chunk 93 optimal weight: 0.0170 chunk 214 optimal weight: 3.9990 chunk 252 optimal weight: 0.0570 chunk 279 optimal weight: 0.6980 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 564 GLN A1101 HIS B 360 ASN B 505 HIS B 613 GLN B 644 GLN B 901 GLN C 207 HIS C 218 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.171833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.130565 restraints weight = 26744.815| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.45 r_work: 0.3206 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25445 Z= 0.100 Angle : 0.510 10.707 34693 Z= 0.261 Chirality : 0.044 0.261 4014 Planarity : 0.003 0.051 4425 Dihedral : 5.579 84.233 3972 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.14 % Allowed : 16.46 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3081 helix: 2.41 (0.20), residues: 687 sheet: 0.91 (0.18), residues: 783 loop : -1.02 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.007 0.000 HIS C 69 PHE 0.024 0.001 PHE A 318 TYR 0.016 0.001 TYR C1067 ARG 0.009 0.000 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 30) link_NAG-ASN : angle 1.55588 ( 90) hydrogen bonds : bond 0.04039 ( 1013) hydrogen bonds : angle 4.33523 ( 2799) SS BOND : bond 0.00397 ( 41) SS BOND : angle 1.99582 ( 82) covalent geometry : bond 0.00227 (25374) covalent geometry : angle 0.49540 (34521) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7371 (mp0) REVERT: A 200 TYR cc_start: 0.8234 (m-80) cc_final: 0.7913 (m-80) REVERT: A 281 GLU cc_start: 0.8332 (pm20) cc_final: 0.7917 (pm20) REVERT: A 443 SER cc_start: 0.8188 (m) cc_final: 0.7867 (p) REVERT: A 592 PHE cc_start: 0.7746 (p90) cc_final: 0.7524 (p90) REVERT: A 904 TYR cc_start: 0.7852 (m-10) cc_final: 0.7609 (m-10) REVERT: B 574 ASP cc_start: 0.8164 (t0) cc_final: 0.7814 (t0) REVERT: B 731 MET cc_start: 0.9274 (ptt) cc_final: 0.8881 (ptt) REVERT: B 1139 ASP cc_start: 0.8118 (t0) cc_final: 0.7813 (t70) REVERT: C 33 THR cc_start: 0.8528 (t) cc_final: 0.8190 (m) REVERT: C 177 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5611 (tmm) REVERT: C 531 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7788 (p) REVERT: C 574 ASP cc_start: 0.8088 (t0) cc_final: 0.7807 (t0) REVERT: C 1113 GLN cc_start: 0.8548 (mt0) cc_final: 0.8311 (mt0) outliers start: 58 outliers final: 40 residues processed: 257 average time/residue: 0.9263 time to fit residues: 292.1213 Evaluate side-chains 238 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 104 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 308 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 52 optimal weight: 0.0770 chunk 77 optimal weight: 1.9990 chunk 287 optimal weight: 0.8980 chunk 251 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A1101 HIS B 644 GLN C 69 HIS C 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.169452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.127943 restraints weight = 26703.904| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.46 r_work: 0.3162 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25445 Z= 0.134 Angle : 0.548 10.954 34693 Z= 0.282 Chirality : 0.045 0.221 4014 Planarity : 0.004 0.052 4425 Dihedral : 5.822 89.285 3972 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.77 % Allowed : 17.20 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3081 helix: 2.52 (0.20), residues: 669 sheet: 0.79 (0.18), residues: 798 loop : -0.97 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.008 0.001 HIS C 69 PHE 0.025 0.001 PHE A 318 TYR 0.016 0.001 TYR C1067 ARG 0.009 0.000 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 30) link_NAG-ASN : angle 1.63087 ( 90) hydrogen bonds : bond 0.04750 ( 1013) hydrogen bonds : angle 4.46580 ( 2799) SS BOND : bond 0.00422 ( 41) SS BOND : angle 2.31982 ( 82) covalent geometry : bond 0.00324 (25374) covalent geometry : angle 0.53129 (34521) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7379 (mp0) REVERT: A 200 TYR cc_start: 0.8299 (m-80) cc_final: 0.7870 (m-80) REVERT: A 281 GLU cc_start: 0.8336 (pm20) cc_final: 0.7931 (pm20) REVERT: A 443 SER cc_start: 0.8203 (m) cc_final: 0.7879 (p) REVERT: A 532 ASN cc_start: 0.8246 (m-40) cc_final: 0.7832 (m110) REVERT: A 904 TYR cc_start: 0.7896 (m-10) cc_final: 0.7673 (m-10) REVERT: B 326 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7681 (mp) REVERT: B 574 ASP cc_start: 0.8199 (t0) cc_final: 0.7827 (t0) REVERT: B 731 MET cc_start: 0.9245 (ptt) cc_final: 0.8963 (ptt) REVERT: B 1139 ASP cc_start: 0.8115 (t0) cc_final: 0.7818 (t70) REVERT: C 33 THR cc_start: 0.8550 (t) cc_final: 0.8211 (m) REVERT: C 177 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5613 (tmm) REVERT: C 472 ILE cc_start: 0.8191 (mm) cc_final: 0.7980 (mp) REVERT: C 531 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7827 (p) REVERT: C 574 ASP cc_start: 0.8135 (t0) cc_final: 0.7834 (t0) REVERT: C 904 TYR cc_start: 0.8075 (m-10) cc_final: 0.6671 (m-80) outliers start: 48 outliers final: 39 residues processed: 235 average time/residue: 1.0060 time to fit residues: 289.5268 Evaluate side-chains 240 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 199 optimal weight: 0.5980 chunk 261 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 0.0040 chunk 117 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 126 optimal weight: 0.0020 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 564 GLN A1101 HIS B 360 ASN C 69 HIS C 207 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.172382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.131356 restraints weight = 26745.318| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.44 r_work: 0.3219 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25445 Z= 0.095 Angle : 0.501 9.781 34693 Z= 0.257 Chirality : 0.043 0.195 4014 Planarity : 0.003 0.053 4425 Dihedral : 5.619 89.917 3972 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.69 % Allowed : 17.35 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 3081 helix: 2.49 (0.20), residues: 687 sheet: 0.85 (0.18), residues: 798 loop : -0.95 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.008 0.001 HIS C 69 PHE 0.026 0.001 PHE A 318 TYR 0.016 0.001 TYR C1067 ARG 0.009 0.000 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 30) link_NAG-ASN : angle 1.51219 ( 90) hydrogen bonds : bond 0.03890 ( 1013) hydrogen bonds : angle 4.30325 ( 2799) SS BOND : bond 0.00394 ( 41) SS BOND : angle 1.98765 ( 82) covalent geometry : bond 0.00211 (25374) covalent geometry : angle 0.48678 (34521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15642.44 seconds wall clock time: 267 minutes 24.65 seconds (16044.65 seconds total)