Starting phenix.real_space_refine on Mon Aug 25 03:04:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ayw_44000/08_2025/9ayw_44000_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ayw_44000/08_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_44000/08_2025/9ayw_44000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ayw_44000/08_2025/9ayw_44000.map" model { file = "/net/cci-nas-00/data/ceres_data/9ayw_44000/08_2025/9ayw_44000_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ayw_44000/08_2025/9ayw_44000_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.069 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24813 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8131 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "B" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8131 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "C" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8131 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.14, per 1000 atoms: 0.21 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: 1.67 Conformation dependent library (CDL) restraints added in 863.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5862 Finding SS restraints... Secondary structure from input PDB file: 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: 1.12 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: 6.15 Time building geometry restraints manager: 2.33 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 22.280 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.200 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (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 ARG 0.016 0.001 ARG C 995 TYR 0.036 0.002 TYR C 453 PHE 0.043 0.002 PHE A 906 TRP 0.034 0.002 TRP B 886 HIS 0.008 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00485 (25374) covalent geometry : angle 0.78371 (34521) SS BOND : bond 0.00719 ( 41) SS BOND : angle 2.69495 ( 82) hydrogen bonds : bond 0.13918 ( 1013) hydrogen bonds : angle 6.18015 ( 2799) link_NAG-ASN : bond 0.00472 ( 30) link_NAG-ASN : angle 2.59361 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.791 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: 0.5075 time to fit residues: 170.9075 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 : 0.739 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0870 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.7364 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.174215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.132659 restraints weight = 26563.011| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.50 r_work: 0.3196 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25445 Z= 0.112 Angle : 0.525 9.333 34693 Z= 0.273 Chirality : 0.044 0.228 4014 Planarity : 0.004 0.062 4425 Dihedral : 6.205 59.819 3974 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.10 % Allowed : 7.37 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.15), residues: 3081 helix: 1.54 (0.20), residues: 663 sheet: 1.03 (0.18), residues: 789 loop : -1.22 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 567 TYR 0.016 0.001 TYR C1067 PHE 0.016 0.001 PHE A 906 TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00256 (25374) covalent geometry : angle 0.50913 (34521) SS BOND : bond 0.00368 ( 41) SS BOND : angle 2.08956 ( 82) hydrogen bonds : bond 0.04658 ( 1013) hydrogen bonds : angle 4.72092 ( 2799) link_NAG-ASN : bond 0.00244 ( 30) link_NAG-ASN : angle 1.69632 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 239 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 592 PHE cc_start: 0.7761 (p90) cc_final: 0.7513 (p90) REVERT: A 735 SER cc_start: 0.9107 (p) cc_final: 0.8898 (t) REVERT: B 30 ASN cc_start: 0.7839 (t0) cc_final: 0.7612 (t0) REVERT: B 282 ASN cc_start: 0.8429 (m-40) cc_final: 0.8081 (m-40) REVERT: B 319 ARG cc_start: 0.7682 (mmm-85) cc_final: 0.7134 (tpt90) REVERT: B 731 MET cc_start: 0.9164 (ptt) cc_final: 0.8719 (ptt) REVERT: B 851 CYS cc_start: 0.8447 (m) cc_final: 0.8183 (m) REVERT: B 1092 GLU cc_start: 0.7984 (pp20) cc_final: 0.7625 (pt0) REVERT: C 776 LYS cc_start: 0.8150 (tttp) cc_final: 0.7908 (tttt) REVERT: C 995 ARG cc_start: 0.7909 (mtt-85) cc_final: 0.7545 (mtm180) outliers start: 30 outliers final: 16 residues processed: 248 average time/residue: 0.4657 time to fit residues: 137.2769 Evaluate side-chains 223 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 900 MET 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 295 optimal weight: 0.5980 chunk 18 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 271 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 286 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN B 339 HIS B 394 ASN B 544 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.168578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126646 restraints weight = 26744.417| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.50 r_work: 0.3153 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25445 Z= 0.189 Angle : 0.607 11.689 34693 Z= 0.312 Chirality : 0.047 0.209 4014 Planarity : 0.004 0.050 4425 Dihedral : 6.021 52.998 3972 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.77 % Allowed : 10.76 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.15), residues: 3081 helix: 1.94 (0.20), residues: 651 sheet: 0.80 (0.18), residues: 762 loop : -1.17 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 567 TYR 0.019 0.001 TYR C1067 PHE 0.033 0.002 PHE A 906 TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00466 (25374) covalent geometry : angle 0.58499 (34521) SS BOND : bond 0.00564 ( 41) SS BOND : angle 2.65231 ( 82) hydrogen bonds : bond 0.05852 ( 1013) hydrogen bonds : angle 4.77656 ( 2799) link_NAG-ASN : bond 0.00232 ( 30) link_NAG-ASN : angle 2.10434 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 223 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 SER cc_start: 0.8255 (m) cc_final: 0.7960 (p) REVERT: A 592 PHE cc_start: 0.7839 (p90) cc_final: 0.7635 (p90) REVERT: A 904 TYR cc_start: 0.7806 (m-10) cc_final: 0.7603 (m-10) REVERT: B 30 ASN cc_start: 0.7963 (t0) cc_final: 0.7730 (t0) REVERT: B 33 THR cc_start: 0.7051 (t) cc_final: 0.6836 (t) REVERT: B 291 CYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7162 (m) REVERT: B 498 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7677 (mtt90) REVERT: B 731 MET cc_start: 0.9195 (ptt) cc_final: 0.8936 (ptt) REVERT: B 995 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7507 (mtt-85) REVERT: C 33 THR cc_start: 0.8563 (t) cc_final: 0.8196 (m) REVERT: C 776 LYS cc_start: 0.8351 (tttp) cc_final: 0.8148 (tttt) outliers start: 48 outliers final: 32 residues processed: 251 average time/residue: 0.4766 time to fit residues: 141.9715 Evaluate side-chains 235 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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 514 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 124 THR Chi-restraints excluded: chain C residue 141 LEU 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 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 295 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 304 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 762 GLN B 321 GLN B1005 GLN B1010 GLN C 218 GLN C 564 GLN C 762 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.171607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.130158 restraints weight = 26435.395| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.41 r_work: 0.3154 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25445 Z= 0.112 Angle : 0.513 10.581 34693 Z= 0.266 Chirality : 0.044 0.205 4014 Planarity : 0.003 0.048 4425 Dihedral : 5.319 54.850 3972 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.80 % Allowed : 12.19 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.15), residues: 3081 helix: 2.14 (0.20), residues: 669 sheet: 0.84 (0.18), residues: 807 loop : -1.14 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 567 TYR 0.016 0.001 TYR C1067 PHE 0.018 0.001 PHE A 318 TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00261 (25374) covalent geometry : angle 0.49682 (34521) SS BOND : bond 0.00429 ( 41) SS BOND : angle 2.10003 ( 82) hydrogen bonds : bond 0.04503 ( 1013) hydrogen bonds : angle 4.49701 ( 2799) link_NAG-ASN : bond 0.00270 ( 30) link_NAG-ASN : angle 1.68812 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8294 (pm20) cc_final: 0.7982 (pm20) REVERT: A 443 SER cc_start: 0.8320 (m) cc_final: 0.7983 (p) REVERT: A 592 PHE cc_start: 0.7817 (p90) cc_final: 0.7592 (p90) REVERT: A 904 TYR cc_start: 0.7843 (m-10) cc_final: 0.7628 (m-10) REVERT: B 30 ASN cc_start: 0.7927 (t0) cc_final: 0.7688 (t0) REVERT: B 306 PHE cc_start: 0.8751 (m-80) cc_final: 0.8530 (m-80) REVERT: B 498 ARG cc_start: 0.7880 (mtt-85) cc_final: 0.7677 (mtt90) REVERT: B 731 MET cc_start: 0.9216 (ptt) cc_final: 0.8843 (ptt) REVERT: C 33 THR cc_start: 0.8509 (t) cc_final: 0.8122 (m) REVERT: C 531 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7682 (p) REVERT: C 776 LYS cc_start: 0.8206 (tttp) cc_final: 0.8004 (tttt) outliers start: 49 outliers final: 34 residues processed: 245 average time/residue: 0.4291 time to fit residues: 127.2958 Evaluate side-chains 241 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 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 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 383 SER 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 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 461 LEU Chi-restraints excluded: chain C residue 531 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 300 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 223 optimal weight: 0.0270 chunk 124 optimal weight: 0.8980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 422 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN B 49 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.171843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.130368 restraints weight = 26595.175| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.45 r_work: 0.3177 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25445 Z= 0.108 Angle : 0.506 10.263 34693 Z= 0.261 Chirality : 0.044 0.202 4014 Planarity : 0.003 0.048 4425 Dihedral : 5.066 53.855 3972 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.03 % Allowed : 13.44 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.15), residues: 3081 helix: 2.33 (0.20), residues: 669 sheet: 0.88 (0.18), residues: 813 loop : -1.07 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 567 TYR 0.016 0.001 TYR C1067 PHE 0.013 0.001 PHE A 906 TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00251 (25374) covalent geometry : angle 0.48699 (34521) SS BOND : bond 0.00403 ( 41) SS BOND : angle 2.08946 ( 82) hydrogen bonds : bond 0.04337 ( 1013) hydrogen bonds : angle 4.39626 ( 2799) link_NAG-ASN : bond 0.00262 ( 30) link_NAG-ASN : angle 1.95578 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 225 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8298 (m-80) cc_final: 0.7908 (m-80) REVERT: A 281 GLU cc_start: 0.8303 (pm20) cc_final: 0.7959 (pm20) REVERT: A 443 SER cc_start: 0.8298 (m) cc_final: 0.7944 (p) REVERT: A 592 PHE cc_start: 0.7818 (p90) cc_final: 0.7559 (p90) REVERT: A 904 TYR cc_start: 0.7793 (m-10) cc_final: 0.7545 (m-10) REVERT: B 30 ASN cc_start: 0.7844 (t0) cc_final: 0.7600 (t0) REVERT: B 306 PHE cc_start: 0.8759 (m-80) cc_final: 0.8523 (m-80) REVERT: B 731 MET cc_start: 0.9245 (ptt) cc_final: 0.8863 (ptt) REVERT: B 1139 ASP cc_start: 0.8113 (t0) cc_final: 0.7812 (t70) REVERT: C 33 THR cc_start: 0.8513 (t) cc_final: 0.8146 (m) REVERT: C 531 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7705 (p) REVERT: C 776 LYS cc_start: 0.8139 (tttp) cc_final: 0.7912 (tttt) REVERT: C 904 TYR cc_start: 0.8016 (m-10) cc_final: 0.6663 (m-80) outliers start: 55 outliers final: 38 residues processed: 259 average time/residue: 0.4275 time to fit residues: 133.7792 Evaluate side-chains 246 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN 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 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 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 900 MET 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 514 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 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 141 LEU 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 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 934 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 89 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 282 optimal weight: 3.9990 chunk 269 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 217 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 297 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN B 321 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.171202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129496 restraints weight = 26648.484| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.49 r_work: 0.3151 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25445 Z= 0.113 Angle : 0.512 10.381 34693 Z= 0.263 Chirality : 0.044 0.196 4014 Planarity : 0.003 0.047 4425 Dihedral : 4.900 53.887 3972 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.58 % Allowed : 13.96 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.15), residues: 3081 helix: 2.42 (0.20), residues: 669 sheet: 0.89 (0.18), residues: 798 loop : -1.02 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 567 TYR 0.016 0.001 TYR C1067 PHE 0.018 0.001 PHE A 318 TRP 0.008 0.001 TRP B 436 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00266 (25374) covalent geometry : angle 0.49221 (34521) SS BOND : bond 0.00405 ( 41) SS BOND : angle 2.01385 ( 82) hydrogen bonds : bond 0.04379 ( 1013) hydrogen bonds : angle 4.37400 ( 2799) link_NAG-ASN : bond 0.00258 ( 30) link_NAG-ASN : angle 2.13846 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 209 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8261 (m-80) cc_final: 0.7889 (m-80) REVERT: A 281 GLU cc_start: 0.8299 (pm20) cc_final: 0.7954 (pm20) REVERT: A 443 SER cc_start: 0.8287 (m) cc_final: 0.7930 (p) REVERT: A 592 PHE cc_start: 0.7818 (p90) cc_final: 0.7586 (p90) REVERT: A 904 TYR cc_start: 0.7863 (m-10) cc_final: 0.7604 (m-10) REVERT: B 30 ASN cc_start: 0.7847 (t0) cc_final: 0.7613 (t0) REVERT: B 306 PHE cc_start: 0.8744 (m-80) cc_final: 0.8464 (m-80) REVERT: B 731 MET cc_start: 0.9239 (ptt) cc_final: 0.8843 (ptt) REVERT: B 1139 ASP cc_start: 0.8110 (t0) cc_final: 0.7805 (t70) REVERT: C 33 THR cc_start: 0.8543 (t) cc_final: 0.8157 (m) REVERT: C 375 PHE cc_start: 0.4471 (OUTLIER) cc_final: 0.3437 (m-80) REVERT: C 531 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7706 (p) REVERT: C 776 LYS cc_start: 0.8147 (tttp) cc_final: 0.7909 (tttt) REVERT: C 904 TYR cc_start: 0.8041 (m-10) cc_final: 0.6698 (m-80) outliers start: 70 outliers final: 49 residues processed: 256 average time/residue: 0.4234 time to fit residues: 131.6865 Evaluate side-chains 254 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN 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 434 ILE Chi-restraints excluded: chain A residue 494 SER 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 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 383 SER Chi-restraints excluded: chain B residue 391 CYS 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 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 916 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 141 LEU 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 375 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 531 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 828 LEU Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 21 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 300 optimal weight: 2.9990 chunk 220 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 251 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.169049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.127049 restraints weight = 26644.599| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.50 r_work: 0.3164 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25445 Z= 0.148 Angle : 0.552 11.370 34693 Z= 0.283 Chirality : 0.045 0.227 4014 Planarity : 0.003 0.046 4425 Dihedral : 5.080 53.347 3972 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.69 % Allowed : 14.36 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.15), residues: 3081 helix: 2.35 (0.20), residues: 669 sheet: 0.89 (0.18), residues: 792 loop : -1.09 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 567 TYR 0.016 0.001 TYR C1067 PHE 0.016 0.001 PHE A 371 TRP 0.008 0.001 TRP B 436 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00360 (25374) covalent geometry : angle 0.53283 (34521) SS BOND : bond 0.00442 ( 41) SS BOND : angle 2.31618 ( 82) hydrogen bonds : bond 0.05031 ( 1013) hydrogen bonds : angle 4.49497 ( 2799) link_NAG-ASN : bond 0.00205 ( 30) link_NAG-ASN : angle 1.86553 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 217 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8300 (pm20) cc_final: 0.7959 (pm20) REVERT: A 443 SER cc_start: 0.8298 (m) cc_final: 0.7952 (p) REVERT: A 904 TYR cc_start: 0.7806 (m-10) cc_final: 0.7596 (m-10) REVERT: B 30 ASN cc_start: 0.7938 (t0) cc_final: 0.7692 (t0) REVERT: B 343 ASN cc_start: 0.7780 (m-40) cc_final: 0.7314 (p0) REVERT: B 498 ARG cc_start: 0.7860 (mtt-85) cc_final: 0.7655 (mtt90) REVERT: B 731 MET cc_start: 0.9233 (ptt) cc_final: 0.8947 (ptt) REVERT: B 1139 ASP cc_start: 0.8061 (t0) cc_final: 0.7758 (t70) REVERT: C 33 THR cc_start: 0.8559 (t) cc_final: 0.8217 (m) REVERT: C 531 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7721 (p) REVERT: C 904 TYR cc_start: 0.8092 (m-10) cc_final: 0.6710 (m-80) outliers start: 73 outliers final: 56 residues processed: 267 average time/residue: 0.4293 time to fit residues: 138.2165 Evaluate side-chains 263 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 206 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN 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 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 494 SER 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 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 177 MET 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 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 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 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 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 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 828 LEU Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 234 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 285 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 263 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A1101 HIS B 321 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3880 r_free = 0.3880 target = 0.168489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.126712 restraints weight = 26643.327| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.46 r_work: 0.3132 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1810 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= 0.151 Angle : 0.561 11.791 34693 Z= 0.288 Chirality : 0.045 0.220 4014 Planarity : 0.004 0.053 4425 Dihedral : 5.160 53.770 3972 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.50 % Allowed : 14.88 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.15), residues: 3081 helix: 2.17 (0.20), residues: 687 sheet: 0.86 (0.18), residues: 792 loop : -1.06 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 567 TYR 0.017 0.001 TYR C1067 PHE 0.019 0.001 PHE A 318 TRP 0.008 0.001 TRP B 436 HIS 0.006 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00371 (25374) covalent geometry : angle 0.54051 (34521) SS BOND : bond 0.00472 ( 41) SS BOND : angle 2.51301 ( 82) hydrogen bonds : bond 0.05026 ( 1013) hydrogen bonds : angle 4.52694 ( 2799) link_NAG-ASN : bond 0.00218 ( 30) link_NAG-ASN : angle 1.84347 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 212 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8298 (pm20) cc_final: 0.7971 (pm20) REVERT: A 443 SER cc_start: 0.8291 (m) cc_final: 0.7946 (p) REVERT: A 532 ASN cc_start: 0.8340 (m-40) cc_final: 0.8108 (m110) REVERT: A 576 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8583 (p) REVERT: A 592 PHE cc_start: 0.7817 (p90) cc_final: 0.7562 (p90) REVERT: A 904 TYR cc_start: 0.7791 (m-10) cc_final: 0.7548 (m-10) REVERT: B 30 ASN cc_start: 0.7977 (t0) cc_final: 0.7715 (t0) REVERT: B 306 PHE cc_start: 0.8531 (m-80) cc_final: 0.8312 (m-80) REVERT: B 343 ASN cc_start: 0.7745 (m-40) cc_final: 0.7399 (p0) REVERT: B 498 ARG cc_start: 0.7894 (mtt-85) cc_final: 0.7665 (mtt90) REVERT: B 731 MET cc_start: 0.9247 (ptt) cc_final: 0.8961 (ptt) REVERT: B 1139 ASP cc_start: 0.8067 (t0) cc_final: 0.7769 (t70) REVERT: C 33 THR cc_start: 0.8570 (t) cc_final: 0.8232 (m) REVERT: C 177 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5566 (tmm) REVERT: C 190 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.8267 (mtm-85) REVERT: C 531 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7698 (p) REVERT: C 574 ASP cc_start: 0.8144 (t0) cc_final: 0.7853 (t0) REVERT: C 904 TYR cc_start: 0.8061 (m-10) cc_final: 0.6656 (m-80) outliers start: 68 outliers final: 55 residues processed: 256 average time/residue: 0.4354 time to fit residues: 134.3979 Evaluate side-chains 263 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN 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 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 494 SER 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 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 177 MET 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 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 916 LEU 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 514 SER Chi-restraints excluded: chain C residue 531 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 934 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 293 optimal weight: 0.9990 chunk 310 optimal weight: 0.0060 chunk 131 optimal weight: 0.0010 chunk 76 optimal weight: 0.9990 chunk 277 optimal weight: 0.7980 chunk 182 optimal weight: 0.8980 chunk 110 optimal weight: 0.3980 chunk 275 optimal weight: 0.8980 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 564 GLN A1101 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1005 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 = 0.3927 r_free = 0.3927 target = 0.173033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.132286 restraints weight = 26698.924| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.41 r_work: 0.3234 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25445 Z= 0.092 Angle : 0.488 10.074 34693 Z= 0.251 Chirality : 0.043 0.175 4014 Planarity : 0.003 0.055 4425 Dihedral : 4.741 54.718 3972 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.69 % Allowed : 15.84 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.15), residues: 3081 helix: 2.63 (0.20), residues: 672 sheet: 0.89 (0.18), residues: 798 loop : -0.96 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 567 TYR 0.016 0.001 TYR C1067 PHE 0.022 0.001 PHE A 318 TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00205 (25374) covalent geometry : angle 0.47290 (34521) SS BOND : bond 0.00405 ( 41) SS BOND : angle 1.94956 ( 82) hydrogen bonds : bond 0.03814 ( 1013) hydrogen bonds : angle 4.29444 ( 2799) link_NAG-ASN : bond 0.00292 ( 30) link_NAG-ASN : angle 1.59213 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 0.628 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: 0.8022 (tm-30) cc_final: 0.7381 (mp0) REVERT: A 200 TYR cc_start: 0.8215 (m-80) cc_final: 0.7910 (m-80) REVERT: A 281 GLU cc_start: 0.8314 (pm20) cc_final: 0.7989 (pm20) REVERT: A 443 SER cc_start: 0.8283 (m) cc_final: 0.7925 (p) REVERT: A 532 ASN cc_start: 0.8222 (m-40) cc_final: 0.7984 (m110) REVERT: A 592 PHE cc_start: 0.7748 (p90) cc_final: 0.7523 (p90) REVERT: A 904 TYR cc_start: 0.7790 (m-10) cc_final: 0.7517 (m-10) REVERT: B 343 ASN cc_start: 0.7662 (m-40) cc_final: 0.7431 (p0) REVERT: B 731 MET cc_start: 0.9257 (ptt) cc_final: 0.8770 (ptt) REVERT: B 1139 ASP cc_start: 0.8115 (t0) cc_final: 0.7793 (t70) REVERT: C 33 THR cc_start: 0.8501 (t) cc_final: 0.8110 (m) REVERT: C 531 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7752 (p) REVERT: C 574 ASP cc_start: 0.8092 (t0) cc_final: 0.7762 (t0) REVERT: C 1113 GLN cc_start: 0.8496 (mt0) cc_final: 0.8264 (mt0) outliers start: 46 outliers final: 31 residues processed: 256 average time/residue: 0.4137 time to fit residues: 128.2972 Evaluate side-chains 238 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 291 CYS 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 551 VAL Chi-restraints excluded: chain A residue 553 THR 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 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 291 CYS 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 859 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 934 ILE 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 90 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 298 optimal weight: 0.5980 chunk 246 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 250 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 26 GLN B 30 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.169137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.127487 restraints weight = 26679.924| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.46 r_work: 0.3167 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25445 Z= 0.147 Angle : 0.552 11.338 34693 Z= 0.284 Chirality : 0.045 0.221 4014 Planarity : 0.003 0.055 4425 Dihedral : 5.004 53.116 3972 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.55 % Allowed : 16.17 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.15), residues: 3081 helix: 2.47 (0.20), residues: 669 sheet: 0.88 (0.18), residues: 795 loop : -1.00 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 567 TYR 0.017 0.001 TYR C1067 PHE 0.024 0.001 PHE A 318 TRP 0.008 0.001 TRP B 436 HIS 0.007 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00359 (25374) covalent geometry : angle 0.53381 (34521) SS BOND : bond 0.00466 ( 41) SS BOND : angle 2.35671 ( 82) hydrogen bonds : bond 0.04938 ( 1013) hydrogen bonds : angle 4.46904 ( 2799) link_NAG-ASN : bond 0.00225 ( 30) link_NAG-ASN : angle 1.72437 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7404 (mp0) REVERT: A 200 TYR cc_start: 0.8316 (m-80) cc_final: 0.7873 (m-80) REVERT: A 281 GLU cc_start: 0.8310 (pm20) cc_final: 0.7995 (pm20) REVERT: A 443 SER cc_start: 0.8272 (m) cc_final: 0.7913 (p) REVERT: A 592 PHE cc_start: 0.7845 (p90) cc_final: 0.7601 (p90) REVERT: A 904 TYR cc_start: 0.7787 (m-10) cc_final: 0.7548 (m-10) REVERT: B 498 ARG cc_start: 0.7860 (mtt-85) cc_final: 0.7657 (mtt90) REVERT: B 731 MET cc_start: 0.9235 (ptt) cc_final: 0.8952 (ptt) REVERT: B 1139 ASP cc_start: 0.8050 (t0) cc_final: 0.7756 (t70) REVERT: C 33 THR cc_start: 0.8576 (t) cc_final: 0.8258 (m) REVERT: C 218 GLN cc_start: 0.8325 (tp40) cc_final: 0.7903 (mp10) REVERT: C 531 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.7753 (p) REVERT: C 574 ASP cc_start: 0.8159 (t0) cc_final: 0.7837 (t0) REVERT: C 904 TYR cc_start: 0.8059 (m-10) cc_final: 0.6659 (m-80) outliers start: 42 outliers final: 36 residues processed: 246 average time/residue: 0.4347 time to fit residues: 128.9948 Evaluate side-chains 242 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 551 VAL Chi-restraints excluded: chain A residue 553 THR 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 1128 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 291 CYS 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 859 THR Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 514 SER 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 934 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 90 optimal weight: 0.7980 chunk 230 optimal weight: 0.9980 chunk 262 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 chunk 190 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 295 optimal weight: 2.9990 chunk 28 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 394 ASN A 564 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 644 GLN B1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.171698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130665 restraints weight = 26677.300| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.42 r_work: 0.3187 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25445 Z= 0.108 Angle : 0.531 22.820 34693 Z= 0.268 Chirality : 0.044 0.258 4014 Planarity : 0.003 0.053 4425 Dihedral : 5.247 57.649 3972 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.80 % Allowed : 15.95 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.15), residues: 3081 helix: 2.62 (0.20), residues: 666 sheet: 0.90 (0.18), residues: 798 loop : -0.95 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 567 TYR 0.015 0.001 TYR C1067 PHE 0.025 0.001 PHE A 318 TRP 0.009 0.001 TRP B 436 HIS 0.007 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00250 (25374) covalent geometry : angle 0.49855 (34521) SS BOND : bond 0.00406 ( 41) SS BOND : angle 2.03789 ( 82) hydrogen bonds : bond 0.04192 ( 1013) hydrogen bonds : angle 4.35029 ( 2799) link_NAG-ASN : bond 0.00415 ( 30) link_NAG-ASN : angle 3.11550 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7030.08 seconds wall clock time: 120 minutes 30.15 seconds (7230.15 seconds total)