Starting phenix.real_space_refine on Mon Aug 25 03:08:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ayx_44001/08_2025/9ayx_44001_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ayx_44001/08_2025/9ayx_44001.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 { model { file = "/net/cci-nas-00/data/ceres_data/9ayx_44001/08_2025/9ayx_44001_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ayx_44001/08_2025/9ayx_44001_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ayx_44001/08_2025/9ayx_44001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ayx_44001/08_2025/9ayx_44001.map" } 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= 0.061 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 41 residue(s): 0.01s 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: 5.31, per 1000 atoms: 0.21 Number of scatterers: 24813 At special positions: 0 Unit cell: (136.08, 129.6, 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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: 1.72 Conformation dependent library (CDL) restraints added in 703.2 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: 69 helices and 47 sheets defined 25.5% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.704A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.701A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.716A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.708A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.636A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.532A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.526A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.511A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.953A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.759A 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: 3.516A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.577A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.794A 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 342 removed outlier: 3.601A pdb=" N VAL B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 342 " --> pdb=" O HIS B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 342' Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.840A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 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: 3.539A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.508A 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 removed outlier: 3.554A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.574A 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: 3.826A 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: 3.502A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.119A 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: 4.256A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN C 343 " --> pdb=" O HIS C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 338 through 343' Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.843A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.661A 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: 3.606A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.687A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) 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: 3.574A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.606A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 842 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.592A 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: 3.817A 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 Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.095A 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: 7.914A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.498A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.600A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 276 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.055A 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: 6.400A 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: 5.225A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.091A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.528A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 435 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.663A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.503A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.246A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.696A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.502A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.855A 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: 4.516A 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: 3.561A pdb=" N THR B 25 " --> pdb=" O HIS B 66 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.516A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.902A 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: 3.558A 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: 3.566A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.441A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.765A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.364A 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 removed outlier: 3.556A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) 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: 3.827A 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: 6.227A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.895A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.588A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.526A 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: 7.425A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.725A 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: 4.527A 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 28 removed outlier: 3.657A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.640A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.867A 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 removed outlier: 6.263A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.160A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.340A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.690A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.445A 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 removed outlier: 3.566A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.644A 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: 6.186A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.404A 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 715 removed outlier: 3.938A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.582A 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: 6.153A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.940A 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: 4.647A 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 974 hydrogen bonds defined for protein. 2703 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: 5.34 Time building geometry restraints manager: 2.27 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: 7930 1.35 - 1.47: 6277 1.47 - 1.59: 11026 1.59 - 1.72: 0 1.72 - 1.84: 141 Bond restraints: 25374 Sorted by residual: bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.68e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.65e+00 ... (remaining 25369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 33554 1.97 - 3.95: 854 3.95 - 5.92: 84 5.92 - 7.89: 19 7.89 - 9.86: 10 Bond angle restraints: 34521 Sorted by residual: angle pdb=" C GLY B 744 " pdb=" N ASP B 745 " pdb=" CA ASP B 745 " ideal model delta sigma weight residual 121.54 131.40 -9.86 1.91e+00 2.74e-01 2.67e+01 angle pdb=" C SER B 112 " pdb=" N LYS B 113 " pdb=" CA LYS B 113 " ideal model delta sigma weight residual 121.54 129.36 -7.82 1.91e+00 2.74e-01 1.68e+01 angle pdb=" C PHE B 32 " pdb=" N THR B 33 " pdb=" CA THR B 33 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.66e+01 angle pdb=" C SER A 112 " pdb=" N LYS A 113 " pdb=" CA LYS A 113 " ideal model delta sigma weight residual 122.61 128.94 -6.33 1.56e+00 4.11e-01 1.65e+01 angle pdb=" CA VAL A 620 " pdb=" CB VAL A 620 " pdb=" CG1 VAL A 620 " ideal model delta sigma weight residual 110.40 117.21 -6.81 1.70e+00 3.46e-01 1.61e+01 ... (remaining 34516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 14066 17.80 - 35.60: 1213 35.60 - 53.41: 180 53.41 - 71.21: 52 71.21 - 89.01: 32 Dihedral angle restraints: 15543 sinusoidal: 6438 harmonic: 9105 Sorted by residual: 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 -163.73 77.73 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -160.89 74.89 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 36.15 56.85 1 1.00e+01 1.00e-02 4.35e+01 ... (remaining 15540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3317 0.068 - 0.135: 636 0.135 - 0.203: 50 0.203 - 0.271: 10 0.271 - 0.339: 1 Chirality restraints: 4014 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL A1128 " pdb=" CA VAL A1128 " pdb=" CG1 VAL A1128 " pdb=" CG2 VAL A1128 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 4011 not shown) Planarity restraints: 4455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 560 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO C 561 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 560 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A 561 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " 0.000 2.00e-02 2.50e+03 2.39e-02 7.14e+00 pdb=" CG ASN C 343 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " -0.029 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " 0.025 2.00e-02 2.50e+03 ... (remaining 4452 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 7439 2.83 - 3.35: 19710 3.35 - 3.87: 39777 3.87 - 4.38: 44633 4.38 - 4.90: 80875 Nonbonded interactions: 192434 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.313 3.040 nonbonded pdb=" OD1 ASP B 294 " pdb=" OG SER B 297 " model vdw 2.323 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.323 3.040 nonbonded pdb=" OE1 GLU C 819 " pdb=" OG SER C1055 " model vdw 2.329 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.329 3.040 ... (remaining 192429 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: 2.290 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.850 Find NCS groups from input model: 0.360 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:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 25445 Z= 0.196 Angle : 0.725 9.863 34693 Z= 0.377 Chirality : 0.052 0.339 4014 Planarity : 0.006 0.108 4425 Dihedral : 13.825 89.010 9558 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.14), residues: 3081 helix: -0.39 (0.17), residues: 717 sheet: 0.44 (0.19), residues: 717 loop : -1.43 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 567 TYR 0.015 0.001 TYR A 28 PHE 0.034 0.002 PHE B 92 TRP 0.023 0.001 TRP B 886 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00404 (25374) covalent geometry : angle 0.70958 (34521) SS BOND : bond 0.00522 ( 41) SS BOND : angle 1.96908 ( 82) hydrogen bonds : bond 0.21463 ( 968) hydrogen bonds : angle 7.74063 ( 2703) link_NAG-ASN : bond 0.00471 ( 30) link_NAG-ASN : angle 2.48505 ( 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 292 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7185 (t70) cc_final: 0.6980 (t70) REVERT: C 1084 ASP cc_start: 0.7971 (t70) cc_final: 0.7703 (t0) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.4378 time to fit residues: 151.8546 Evaluate side-chains 217 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 314 GLN A 613 GLN B 188 ASN B 207 HIS B 370 ASN B 394 ASN B 544 ASN B 564 GLN B 613 GLN B1101 HIS C 121 ASN C 354 ASN C 675 GLN C 901 GLN C1010 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.180956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.129132 restraints weight = 26909.105| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.61 r_work: 0.3184 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 25445 Z= 0.222 Angle : 0.639 8.320 34693 Z= 0.328 Chirality : 0.048 0.245 4014 Planarity : 0.005 0.074 4425 Dihedral : 6.364 59.915 3972 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.73 % Allowed : 7.70 % Favored : 90.57 % 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 (0.14), residues: 3081 helix: 1.08 (0.20), residues: 675 sheet: 0.60 (0.18), residues: 750 loop : -1.37 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 319 TYR 0.018 0.002 TYR A1067 PHE 0.050 0.002 PHE B 92 TRP 0.015 0.002 TRP A 886 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00550 (25374) covalent geometry : angle 0.62175 (34521) SS BOND : bond 0.00465 ( 41) SS BOND : angle 2.04766 ( 82) hydrogen bonds : bond 0.06538 ( 968) hydrogen bonds : angle 5.40682 ( 2703) link_NAG-ASN : bond 0.00484 ( 30) link_NAG-ASN : angle 2.25748 ( 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 296 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 249 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 238 PHE cc_start: 0.5341 (OUTLIER) cc_final: 0.3186 (t80) REVERT: A 531 THR cc_start: 0.9213 (OUTLIER) cc_final: 0.8997 (t) REVERT: A 574 ASP cc_start: 0.8266 (t70) cc_final: 0.7959 (t0) REVERT: B 904 TYR cc_start: 0.7952 (m-10) cc_final: 0.7281 (m-10) REVERT: C 378 LYS cc_start: 0.7436 (pttt) cc_final: 0.7142 (pttt) REVERT: C 586 ASP cc_start: 0.8179 (m-30) cc_final: 0.7755 (m-30) REVERT: C 1084 ASP cc_start: 0.8746 (t70) cc_final: 0.8279 (t0) outliers start: 47 outliers final: 19 residues processed: 280 average time/residue: 0.3717 time to fit residues: 126.1680 Evaluate side-chains 230 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 295 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 271 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 564 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 52 HIS C 207 HIS C 339 HIS C 414 GLN C 675 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.182286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.130914 restraints weight = 26907.399| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.63 r_work: 0.3206 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25445 Z= 0.157 Angle : 0.585 13.862 34693 Z= 0.298 Chirality : 0.047 0.457 4014 Planarity : 0.004 0.062 4425 Dihedral : 5.995 57.245 3972 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.21 % Allowed : 10.61 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.15), residues: 3081 helix: 1.59 (0.21), residues: 672 sheet: 0.55 (0.18), residues: 762 loop : -1.29 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 567 TYR 0.016 0.001 TYR A1067 PHE 0.028 0.001 PHE B 92 TRP 0.011 0.001 TRP A 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00383 (25374) covalent geometry : angle 0.56288 (34521) SS BOND : bond 0.00473 ( 41) SS BOND : angle 1.92816 ( 82) hydrogen bonds : bond 0.05477 ( 968) hydrogen bonds : angle 5.07500 ( 2703) link_NAG-ASN : bond 0.00345 ( 30) link_NAG-ASN : angle 2.68709 ( 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 284 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 224 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 201 PHE cc_start: 0.6023 (t80) cc_final: 0.5745 (t80) REVERT: A 326 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.7058 (mp) REVERT: A 392 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.5314 (p90) REVERT: A 574 ASP cc_start: 0.8268 (t70) cc_final: 0.7962 (t0) REVERT: B 207 HIS cc_start: 0.8027 (t-170) cc_final: 0.7802 (t-90) REVERT: B 378 LYS cc_start: 0.6629 (tppt) cc_final: 0.5304 (mptp) REVERT: B 619 GLU cc_start: 0.7972 (mp0) cc_final: 0.7726 (mp0) REVERT: B 904 TYR cc_start: 0.7864 (m-10) cc_final: 0.7116 (m-10) REVERT: C 53 ASP cc_start: 0.7465 (t70) cc_final: 0.7220 (t0) REVERT: C 378 LYS cc_start: 0.7208 (pttt) cc_final: 0.6949 (pttt) REVERT: C 564 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.6794 (mm-40) REVERT: C 586 ASP cc_start: 0.8108 (m-30) cc_final: 0.7826 (m-30) REVERT: C 935 GLN cc_start: 0.7487 (tt0) cc_final: 0.7176 (tt0) REVERT: C 1084 ASP cc_start: 0.8721 (t70) cc_final: 0.8220 (t0) outliers start: 60 outliers final: 26 residues processed: 271 average time/residue: 0.3869 time to fit residues: 127.8994 Evaluate side-chains 240 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 0.7980 chunk 216 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 304 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 564 GLN B 81 ASN B 394 ASN B 644 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS B1101 HIS B1135 ASN C 52 HIS C 414 GLN C 675 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.184062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.133366 restraints weight = 26686.664| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.36 r_work: 0.3244 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25445 Z= 0.109 Angle : 0.514 10.321 34693 Z= 0.263 Chirality : 0.044 0.266 4014 Planarity : 0.003 0.056 4425 Dihedral : 5.412 52.337 3972 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.43 % Allowed : 11.23 % Favored : 86.34 % 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: 0.05 (0.15), residues: 3081 helix: 2.01 (0.20), residues: 681 sheet: 0.63 (0.18), residues: 768 loop : -1.18 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.014 0.001 TYR A1067 PHE 0.017 0.001 PHE B 592 TRP 0.009 0.001 TRP C 886 HIS 0.002 0.000 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00250 (25374) covalent geometry : angle 0.49836 (34521) SS BOND : bond 0.00479 ( 41) SS BOND : angle 1.62419 ( 82) hydrogen bonds : bond 0.04488 ( 968) hydrogen bonds : angle 4.75779 ( 2703) link_NAG-ASN : bond 0.00485 ( 30) link_NAG-ASN : angle 2.03047 ( 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 305 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 239 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 201 PHE cc_start: 0.5991 (t80) cc_final: 0.5675 (t80) REVERT: A 291 CYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7794 (m) REVERT: A 326 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6956 (mp) REVERT: A 392 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.5385 (p90) REVERT: A 574 ASP cc_start: 0.8252 (t70) cc_final: 0.7964 (t70) REVERT: A 1127 ASP cc_start: 0.8078 (m-30) cc_final: 0.7859 (m-30) REVERT: B 177 MET cc_start: 0.3850 (OUTLIER) cc_final: 0.2395 (pp-130) REVERT: B 207 HIS cc_start: 0.7947 (t-170) cc_final: 0.7663 (t-90) REVERT: B 347 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8398 (m-10) REVERT: B 378 LYS cc_start: 0.6656 (tppt) cc_final: 0.5364 (mptp) REVERT: B 406 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.6486 (mm-30) REVERT: B 904 TYR cc_start: 0.7826 (m-10) cc_final: 0.7011 (m-10) REVERT: C 118 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.4845 (OUTLIER) REVERT: C 357 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7511 (mtp180) REVERT: C 378 LYS cc_start: 0.6988 (pttt) cc_final: 0.6730 (pttt) REVERT: C 564 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.6712 (mm-40) REVERT: C 586 ASP cc_start: 0.7864 (m-30) cc_final: 0.7525 (m-30) REVERT: C 661 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7644 (tp30) REVERT: C 935 GLN cc_start: 0.7271 (tt0) cc_final: 0.6951 (tt0) REVERT: C 1084 ASP cc_start: 0.8687 (t70) cc_final: 0.8192 (t0) outliers start: 66 outliers final: 27 residues processed: 285 average time/residue: 0.3898 time to fit residues: 135.2514 Evaluate side-chains 254 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 300 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 223 optimal weight: 10.0000 chunk 124 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 540 ASN A 564 GLN B 394 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 52 HIS C 414 GLN C 540 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.183567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.132836 restraints weight = 26661.995| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.22 r_work: 0.3242 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25445 Z= 0.112 Angle : 0.511 10.116 34693 Z= 0.260 Chirality : 0.044 0.256 4014 Planarity : 0.003 0.054 4425 Dihedral : 5.224 51.393 3972 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.28 % Allowed : 12.27 % Favored : 85.45 % 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: 0.18 (0.15), residues: 3081 helix: 2.11 (0.20), residues: 696 sheet: 0.67 (0.18), residues: 765 loop : -1.09 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.014 0.001 TYR A1067 PHE 0.026 0.001 PHE B 140 TRP 0.008 0.001 TRP C 886 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00263 (25374) covalent geometry : angle 0.49467 (34521) SS BOND : bond 0.00449 ( 41) SS BOND : angle 1.71373 ( 82) hydrogen bonds : bond 0.04506 ( 968) hydrogen bonds : angle 4.69801 ( 2703) link_NAG-ASN : bond 0.00413 ( 30) link_NAG-ASN : angle 1.99120 ( 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 288 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 226 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.6921 (tm-30) cc_final: 0.5600 (mp0) REVERT: A 201 PHE cc_start: 0.5898 (t80) cc_final: 0.5547 (t80) REVERT: A 290 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8464 (m-30) REVERT: A 291 CYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7682 (m) REVERT: A 389 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6984 (p0) REVERT: A 392 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.5491 (p90) REVERT: A 440 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8072 (ttpp) REVERT: A 532 ASN cc_start: 0.8896 (t0) cc_final: 0.8658 (m-40) REVERT: A 574 ASP cc_start: 0.8258 (t70) cc_final: 0.7973 (t70) REVERT: B 177 MET cc_start: 0.3912 (OUTLIER) cc_final: 0.2330 (pp-130) REVERT: B 347 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8504 (m-10) REVERT: B 406 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.6532 (mm-30) REVERT: B 904 TYR cc_start: 0.7839 (m-10) cc_final: 0.6977 (m-10) REVERT: C 118 LEU cc_start: 0.5675 (OUTLIER) cc_final: 0.4888 (mm) REVERT: C 357 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7538 (mtp180) REVERT: C 378 LYS cc_start: 0.7013 (pttt) cc_final: 0.6803 (pttt) REVERT: C 661 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7659 (tp30) REVERT: C 935 GLN cc_start: 0.7724 (tt0) cc_final: 0.7385 (tt0) REVERT: C 1084 ASP cc_start: 0.8709 (t70) cc_final: 0.8168 (t0) outliers start: 62 outliers final: 36 residues processed: 273 average time/residue: 0.3714 time to fit residues: 123.3408 Evaluate side-chains 255 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 210 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 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: 3.9990 chunk 172 optimal weight: 4.9990 chunk 282 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 154 optimal weight: 0.0030 chunk 217 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 297 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 405 ASN A 564 GLN A 710 ASN B 564 GLN B1101 HIS C 49 HIS C 52 HIS C 69 HIS C 414 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.175550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118267 restraints weight = 26805.386| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.37 r_work: 0.3096 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 25445 Z= 0.267 Angle : 0.663 11.600 34693 Z= 0.340 Chirality : 0.050 0.245 4014 Planarity : 0.004 0.054 4425 Dihedral : 6.007 58.569 3972 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.17 % Allowed : 12.52 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.15), residues: 3081 helix: 1.56 (0.20), residues: 690 sheet: 0.47 (0.18), residues: 765 loop : -1.23 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1039 TYR 0.023 0.002 TYR B 351 PHE 0.026 0.002 PHE A 58 TRP 0.016 0.002 TRP C 104 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00671 (25374) covalent geometry : angle 0.64302 (34521) SS BOND : bond 0.00573 ( 41) SS BOND : angle 2.59988 ( 82) hydrogen bonds : bond 0.06716 ( 968) hydrogen bonds : angle 5.11815 ( 2703) link_NAG-ASN : bond 0.00377 ( 30) link_NAG-ASN : angle 2.21312 ( 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 319 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 233 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8604 (m) cc_final: 0.8243 (p) REVERT: A 169 GLU cc_start: 0.6947 (tm-30) cc_final: 0.5564 (mp0) REVERT: A 291 CYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7631 (m) REVERT: A 392 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.5305 (p90) REVERT: A 440 LYS cc_start: 0.8593 (mmtm) cc_final: 0.8073 (ttpp) REVERT: A 532 ASN cc_start: 0.8969 (t0) cc_final: 0.8748 (m-40) REVERT: A 574 ASP cc_start: 0.8318 (t70) cc_final: 0.7959 (t0) REVERT: A 646 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8173 (mpp80) REVERT: B 351 TYR cc_start: 0.7662 (p90) cc_final: 0.7415 (p90) REVERT: B 378 LYS cc_start: 0.7093 (tppt) cc_final: 0.6039 (mptt) REVERT: B 564 GLN cc_start: 0.7765 (tp40) cc_final: 0.7482 (mm110) REVERT: B 1002 GLN cc_start: 0.8171 (tp-100) cc_final: 0.7829 (tt0) REVERT: C 357 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7619 (mtp180) REVERT: C 420 ASP cc_start: 0.7872 (m-30) cc_final: 0.7522 (m-30) REVERT: C 619 GLU cc_start: 0.7168 (tt0) cc_final: 0.6674 (tm-30) REVERT: C 808 ASP cc_start: 0.7534 (p0) cc_final: 0.6783 (t0) REVERT: C 935 GLN cc_start: 0.7862 (tt0) cc_final: 0.7471 (tt0) REVERT: C 1002 GLN cc_start: 0.8009 (tt0) cc_final: 0.7731 (tp40) REVERT: C 1084 ASP cc_start: 0.8827 (t70) cc_final: 0.8308 (t0) outliers start: 86 outliers final: 48 residues processed: 297 average time/residue: 0.3668 time to fit residues: 132.4836 Evaluate side-chains 262 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 210 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 21 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 79 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 300 optimal weight: 0.6980 chunk 220 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 564 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 414 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.180954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.131182 restraints weight = 26654.864| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.23 r_work: 0.3228 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2524 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 : 0.531 11.444 34693 Z= 0.269 Chirality : 0.044 0.275 4014 Planarity : 0.004 0.054 4425 Dihedral : 5.496 52.159 3972 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.47 % Allowed : 13.52 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.09 (0.15), residues: 3081 helix: 2.16 (0.21), residues: 678 sheet: 0.54 (0.18), residues: 771 loop : -1.15 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 190 TYR 0.019 0.001 TYR B 351 PHE 0.025 0.001 PHE B 541 TRP 0.010 0.001 TRP C 886 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00259 (25374) covalent geometry : angle 0.51327 (34521) SS BOND : bond 0.00474 ( 41) SS BOND : angle 1.63921 ( 82) hydrogen bonds : bond 0.04513 ( 968) hydrogen bonds : angle 4.75207 ( 2703) link_NAG-ASN : bond 0.00329 ( 30) link_NAG-ASN : angle 2.32099 ( 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 297 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 230 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7114 (t0) cc_final: 0.6702 (m-40) REVERT: A 169 GLU cc_start: 0.6952 (tm-30) cc_final: 0.5686 (mp0) REVERT: A 291 CYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7631 (m) REVERT: A 392 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.5524 (p90) REVERT: A 440 LYS cc_start: 0.8496 (mmtm) cc_final: 0.8133 (ttpp) REVERT: A 532 ASN cc_start: 0.8948 (t0) cc_final: 0.8735 (m-40) REVERT: A 574 ASP cc_start: 0.8323 (t70) cc_final: 0.8003 (t70) REVERT: B 378 LYS cc_start: 0.7273 (tppt) cc_final: 0.6193 (mptt) REVERT: B 394 ASN cc_start: 0.8012 (m-40) cc_final: 0.7706 (m-40) REVERT: B 564 GLN cc_start: 0.7693 (tp40) cc_final: 0.7352 (mm110) REVERT: B 814 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7970 (mppt) REVERT: B 904 TYR cc_start: 0.7792 (m-10) cc_final: 0.6791 (m-10) REVERT: C 357 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7669 (mtp180) REVERT: C 420 ASP cc_start: 0.7958 (m-30) cc_final: 0.7588 (m-30) REVERT: C 449 TYR cc_start: 0.7406 (m-10) cc_final: 0.7034 (m-80) REVERT: C 661 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7765 (tp30) REVERT: C 808 ASP cc_start: 0.7559 (p0) cc_final: 0.6770 (t0) REVERT: C 935 GLN cc_start: 0.7809 (tt0) cc_final: 0.7433 (tt0) REVERT: C 1084 ASP cc_start: 0.8779 (t70) cc_final: 0.8236 (t0) REVERT: C 1138 TYR cc_start: 0.8282 (t80) cc_final: 0.7918 (t80) outliers start: 67 outliers final: 37 residues processed: 282 average time/residue: 0.3581 time to fit residues: 123.7919 Evaluate side-chains 255 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 234 optimal weight: 0.6980 chunk 185 optimal weight: 0.6980 chunk 225 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 285 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 137 optimal weight: 0.0060 chunk 263 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 564 GLN A 675 GLN B 30 ASN B 188 ASN B 755 GLN B1101 HIS C 414 GLN C 437 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.180750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.129337 restraints weight = 26735.245| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.60 r_work: 0.3209 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25445 Z= 0.132 Angle : 0.541 10.141 34693 Z= 0.276 Chirality : 0.045 0.254 4014 Planarity : 0.004 0.053 4425 Dihedral : 5.424 50.277 3972 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.54 % Allowed : 13.66 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.15 (0.15), residues: 3081 helix: 2.09 (0.20), residues: 696 sheet: 0.57 (0.18), residues: 771 loop : -1.08 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 190 TYR 0.017 0.001 TYR C 904 PHE 0.021 0.001 PHE C 194 TRP 0.008 0.001 TRP C 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00318 (25374) covalent geometry : angle 0.52392 (34521) SS BOND : bond 0.00478 ( 41) SS BOND : angle 1.84584 ( 82) hydrogen bonds : bond 0.04871 ( 968) hydrogen bonds : angle 4.73746 ( 2703) link_NAG-ASN : bond 0.00311 ( 30) link_NAG-ASN : angle 2.14411 ( 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 288 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 219 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7093 (t0) cc_final: 0.6720 (m-40) REVERT: A 169 GLU cc_start: 0.6971 (tm-30) cc_final: 0.5729 (mp0) REVERT: A 291 CYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7558 (m) REVERT: A 392 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.5665 (p90) REVERT: A 440 LYS cc_start: 0.8507 (mmtm) cc_final: 0.8142 (tmtt) REVERT: A 532 ASN cc_start: 0.8986 (t0) cc_final: 0.8708 (m-40) REVERT: A 574 ASP cc_start: 0.8360 (t70) cc_final: 0.8020 (t70) REVERT: B 347 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8525 (m-10) REVERT: B 378 LYS cc_start: 0.7429 (tppt) cc_final: 0.6365 (mptt) REVERT: B 394 ASN cc_start: 0.8094 (m-40) cc_final: 0.7885 (m-40) REVERT: B 564 GLN cc_start: 0.7692 (tp40) cc_final: 0.7397 (mm110) REVERT: B 814 LYS cc_start: 0.8372 (mmtt) cc_final: 0.7983 (mppt) REVERT: B 904 TYR cc_start: 0.7834 (m-10) cc_final: 0.6894 (m-10) REVERT: C 357 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7691 (mtp180) REVERT: C 420 ASP cc_start: 0.7909 (m-30) cc_final: 0.7410 (m-30) REVERT: C 449 TYR cc_start: 0.7457 (m-10) cc_final: 0.7052 (m-80) REVERT: C 586 ASP cc_start: 0.7928 (m-30) cc_final: 0.7616 (m-30) REVERT: C 786 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.8014 (pttt) REVERT: C 808 ASP cc_start: 0.7557 (p0) cc_final: 0.6820 (t0) REVERT: C 935 GLN cc_start: 0.7883 (tt0) cc_final: 0.7500 (tt0) REVERT: C 1084 ASP cc_start: 0.8796 (t70) cc_final: 0.8258 (t0) outliers start: 69 outliers final: 43 residues processed: 271 average time/residue: 0.4462 time to fit residues: 146.6484 Evaluate side-chains 262 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 285 optimal weight: 3.9990 chunk 293 optimal weight: 0.9980 chunk 310 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 277 optimal weight: 0.6980 chunk 182 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 675 GLN B 755 GLN B1101 HIS C 414 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.181254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.129923 restraints weight = 26815.837| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.60 r_work: 0.3229 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25445 Z= 0.126 Angle : 0.539 10.937 34693 Z= 0.273 Chirality : 0.045 0.255 4014 Planarity : 0.004 0.052 4425 Dihedral : 5.388 50.990 3972 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.14 % Allowed : 14.25 % Favored : 83.61 % 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: 0.18 (0.15), residues: 3081 helix: 2.11 (0.20), residues: 696 sheet: 0.61 (0.18), residues: 771 loop : -1.07 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 190 TYR 0.025 0.001 TYR B 351 PHE 0.023 0.001 PHE B 541 TRP 0.008 0.001 TRP C 886 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00303 (25374) covalent geometry : angle 0.52161 (34521) SS BOND : bond 0.00457 ( 41) SS BOND : angle 1.72113 ( 82) hydrogen bonds : bond 0.04725 ( 968) hydrogen bonds : angle 4.70479 ( 2703) link_NAG-ASN : bond 0.00336 ( 30) link_NAG-ASN : angle 2.25369 ( 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 275 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 217 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7182 (t0) cc_final: 0.6903 (m-40) REVERT: A 169 GLU cc_start: 0.6985 (tm-30) cc_final: 0.5774 (mp0) REVERT: A 291 CYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7549 (m) REVERT: A 392 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.5669 (p90) REVERT: A 440 LYS cc_start: 0.8509 (mmtm) cc_final: 0.8150 (tmtt) REVERT: A 532 ASN cc_start: 0.9006 (t0) cc_final: 0.8717 (m-40) REVERT: A 574 ASP cc_start: 0.8316 (t70) cc_final: 0.7992 (t70) REVERT: B 95 THR cc_start: 0.8759 (p) cc_final: 0.8468 (t) REVERT: B 177 MET cc_start: 0.2828 (OUTLIER) cc_final: 0.1754 (pp-130) REVERT: B 347 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8525 (m-10) REVERT: B 394 ASN cc_start: 0.8064 (m-40) cc_final: 0.7807 (m-40) REVERT: B 564 GLN cc_start: 0.7656 (tp40) cc_final: 0.7371 (mm110) REVERT: B 814 LYS cc_start: 0.8372 (mmtt) cc_final: 0.7979 (mppt) REVERT: B 904 TYR cc_start: 0.7869 (m-10) cc_final: 0.6937 (m-10) REVERT: C 271 GLN cc_start: 0.8207 (mt0) cc_final: 0.7986 (mt0) REVERT: C 319 ARG cc_start: 0.7765 (mtp-110) cc_final: 0.7198 (ttm110) REVERT: C 357 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7698 (mtp180) REVERT: C 420 ASP cc_start: 0.7901 (m-30) cc_final: 0.7535 (m-30) REVERT: C 586 ASP cc_start: 0.7920 (m-30) cc_final: 0.7352 (m-30) REVERT: C 786 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7993 (pttt) REVERT: C 808 ASP cc_start: 0.7475 (p0) cc_final: 0.6763 (t0) REVERT: C 935 GLN cc_start: 0.7839 (tt0) cc_final: 0.7462 (tt0) REVERT: C 1084 ASP cc_start: 0.8798 (t70) cc_final: 0.8256 (t0) outliers start: 58 outliers final: 41 residues processed: 262 average time/residue: 0.4619 time to fit residues: 145.6872 Evaluate side-chains 258 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 104 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 284 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 120 optimal weight: 0.0000 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 675 GLN B 755 GLN B1101 HIS C 218 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.180400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128958 restraints weight = 26769.664| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.60 r_work: 0.3217 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25445 Z= 0.154 Angle : 0.684 56.769 34693 Z= 0.368 Chirality : 0.045 0.250 4014 Planarity : 0.004 0.063 4425 Dihedral : 5.407 50.900 3972 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.92 % Allowed : 14.70 % Favored : 83.39 % 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: 0.14 (0.15), residues: 3081 helix: 2.06 (0.20), residues: 696 sheet: 0.59 (0.18), residues: 771 loop : -1.08 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 190 TYR 0.024 0.001 TYR C 904 PHE 0.049 0.002 PHE C 32 TRP 0.008 0.001 TRP C 886 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00377 (25374) covalent geometry : angle 0.65996 (34521) SS BOND : bond 0.00471 ( 41) SS BOND : angle 1.80359 ( 82) hydrogen bonds : bond 0.04952 ( 968) hydrogen bonds : angle 4.72701 ( 2703) link_NAG-ASN : bond 0.00408 ( 30) link_NAG-ASN : angle 3.18533 ( 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 267 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 215 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7192 (t0) cc_final: 0.6913 (m-40) REVERT: A 169 GLU cc_start: 0.6978 (tm-30) cc_final: 0.5764 (mp0) REVERT: A 291 CYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7596 (m) REVERT: A 392 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.5753 (p90) REVERT: A 440 LYS cc_start: 0.8513 (mmtm) cc_final: 0.8148 (tmtt) REVERT: A 532 ASN cc_start: 0.9001 (t0) cc_final: 0.8718 (m-40) REVERT: A 574 ASP cc_start: 0.8344 (t70) cc_final: 0.8009 (t70) REVERT: B 95 THR cc_start: 0.8761 (p) cc_final: 0.8467 (t) REVERT: B 177 MET cc_start: 0.2735 (OUTLIER) cc_final: 0.1703 (pp-130) REVERT: B 347 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8526 (m-10) REVERT: B 351 TYR cc_start: 0.7682 (p90) cc_final: 0.7355 (p90) REVERT: B 394 ASN cc_start: 0.8071 (m-40) cc_final: 0.7797 (m-40) REVERT: B 564 GLN cc_start: 0.7652 (tp40) cc_final: 0.7365 (mm110) REVERT: B 814 LYS cc_start: 0.8372 (mmtt) cc_final: 0.7978 (mppt) REVERT: B 904 TYR cc_start: 0.7884 (m-10) cc_final: 0.6971 (m-10) REVERT: C 271 GLN cc_start: 0.8212 (mt0) cc_final: 0.7912 (mt0) REVERT: C 319 ARG cc_start: 0.7780 (mtp-110) cc_final: 0.7210 (ttm110) REVERT: C 357 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7715 (mtp180) REVERT: C 420 ASP cc_start: 0.7896 (m-30) cc_final: 0.7528 (m-30) REVERT: C 586 ASP cc_start: 0.7972 (m-30) cc_final: 0.7437 (m-30) REVERT: C 808 ASP cc_start: 0.7464 (p0) cc_final: 0.6756 (t0) REVERT: C 902 MET cc_start: 0.9036 (mmp) cc_final: 0.8785 (mmp) REVERT: C 935 GLN cc_start: 0.7862 (tt0) cc_final: 0.7472 (tt0) REVERT: C 1084 ASP cc_start: 0.8812 (t70) cc_final: 0.8272 (t0) outliers start: 52 outliers final: 43 residues processed: 256 average time/residue: 0.4486 time to fit residues: 138.8677 Evaluate side-chains 261 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 90 optimal weight: 0.9980 chunk 230 optimal weight: 0.9990 chunk 262 optimal weight: 0.2980 chunk 189 optimal weight: 0.7980 chunk 249 optimal weight: 9.9990 chunk 190 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 295 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 675 GLN B 755 GLN B1101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.181931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.130580 restraints weight = 26814.974| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.55 r_work: 0.3246 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25445 Z= 0.112 Angle : 0.520 10.633 34693 Z= 0.265 Chirality : 0.044 0.255 4014 Planarity : 0.004 0.055 4425 Dihedral : 5.139 51.551 3972 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.95 % Allowed : 14.73 % Favored : 83.31 % 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: 2.28 (0.21), residues: 678 sheet: 0.67 (0.18), residues: 771 loop : -1.07 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 190 TYR 0.019 0.001 TYR C 904 PHE 0.024 0.001 PHE B 541 TRP 0.008 0.001 TRP C 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00260 (25374) covalent geometry : angle 0.50581 (34521) SS BOND : bond 0.00442 ( 41) SS BOND : angle 1.55463 ( 82) hydrogen bonds : bond 0.04425 ( 968) hydrogen bonds : angle 4.63945 ( 2703) link_NAG-ASN : bond 0.00345 ( 30) link_NAG-ASN : angle 2.02184 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7435.71 seconds wall clock time: 127 minutes 21.08 seconds (7641.08 seconds total)