Starting phenix.real_space_refine on Sat Jul 4 13:14:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h3m_34469/07_2026/8h3m_34469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3m_34469/07_2026/8h3m_34469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8h3m_34469/07_2026/8h3m_34469.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h3m_34469/07_2026/8h3m_34469.cif" model { file = "/net/cci-nas-00/data/ceres_data/8h3m_34469/07_2026/8h3m_34469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3m_34469/07_2026/8h3m_34469.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h3m_34469/07_2026/8h3m_34469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3m_34469/07_2026/8h3m_34469.map" } resolution = 2.48 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= 0.000 sd= 0.001 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 88 5.16 5 C 13420 2.51 5 N 3458 2.21 5 O 3970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20936 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 7039 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 47, 'TRANS': 862} Chain breaks: 10 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 255 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain breaks: 3 Chain: "B" Number of atoms: 5883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 5883 Classifications: {'peptide': 763} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 40, 'TRANS': 722} Chain breaks: 13 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 7213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7213 Classifications: {'peptide': 930} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 48, 'TRANS': 881} Chain breaks: 13 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "H" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 238 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain breaks: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 4.52, per 1000 atoms: 0.22 Number of scatterers: 20936 At special positions: 0 Unit cell: (131.6, 119.568, 168.448, 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 88 16.00 O 3970 8.00 N 3458 7.00 C 13420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 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 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " 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=2.02 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 B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 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 A1074 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 343 " " NAG A1309 " - " ASN A 717 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B1134 " " NAG B1303 " - " ASN B1098 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B 717 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C1134 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 717 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 986.9 milliseconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4998 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 41 sheets defined 28.0% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.747A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.517A 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 849 through 856 removed outlier: 3.528A pdb=" N LYS A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.067A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 4.104A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.933A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.509A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.513A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.528A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.076A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.067A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.608A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.687A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.019A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.763A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.680A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.901A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 783 removed outlier: 3.982A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.953A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.148A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.736A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.752A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.127A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.842A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.772A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.193A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.497A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.080A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.957A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.664A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.664A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.413A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.649A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.445A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.552A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.947A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AB9, first strand: chain 'B' and resid 170 through 171 removed outlier: 3.563A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 191 through 195 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 318 removed outlier: 7.337A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 538 through 543 Processing sheet with id=AC4, first strand: chain 'B' and resid 566 through 567 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.207A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.620A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.620A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.454A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.660A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.154A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.928A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.033A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.568A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AD8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.361A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.918A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.605A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.462A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.449A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1094 through 1097 961 hydrogen bonds defined for protein. 2592 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: 4.97 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: 6624 1.35 - 1.48: 5598 1.48 - 1.60: 9056 1.60 - 1.73: 0 1.73 - 1.86: 113 Bond restraints: 21391 Sorted by residual: bond pdb=" N ASN A1108 " pdb=" CA ASN A1108 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.22e-02 6.72e+03 8.36e+00 bond pdb=" CG PRO C 426 " pdb=" CD PRO C 426 " ideal model delta sigma weight residual 1.503 1.412 0.091 3.40e-02 8.65e+02 7.15e+00 bond pdb=" N GLN A1106 " pdb=" CA GLN A1106 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.34e-02 5.57e+03 6.15e+00 bond pdb=" N ARG A1107 " pdb=" CA ARG A1107 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.33e-02 5.65e+03 5.75e+00 bond pdb=" CA ASN A 121 " pdb=" CB ASN A 121 " ideal model delta sigma weight residual 1.525 1.556 -0.031 1.29e-02 6.01e+03 5.74e+00 ... (remaining 21386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 28787 2.56 - 5.11: 282 5.11 - 7.67: 20 7.67 - 10.23: 5 10.23 - 12.78: 1 Bond angle restraints: 29095 Sorted by residual: angle pdb=" N PRO C 426 " pdb=" CD PRO C 426 " pdb=" CG PRO C 426 " ideal model delta sigma weight residual 103.20 93.11 10.09 1.50e+00 4.44e-01 4.52e+01 angle pdb=" CA PRO A 521 " pdb=" N PRO A 521 " pdb=" CD PRO A 521 " ideal model delta sigma weight residual 112.00 102.79 9.21 1.40e+00 5.10e-01 4.33e+01 angle pdb=" CA PRO C 426 " pdb=" CB PRO C 426 " pdb=" CG PRO C 426 " ideal model delta sigma weight residual 104.50 94.79 9.71 1.90e+00 2.77e-01 2.61e+01 angle pdb=" C GLU B 619 " pdb=" CA GLU B 619 " pdb=" CB GLU B 619 " ideal model delta sigma weight residual 109.29 115.76 -6.47 1.51e+00 4.39e-01 1.83e+01 angle pdb=" CA PRO C 426 " pdb=" N PRO C 426 " pdb=" CD PRO C 426 " ideal model delta sigma weight residual 112.00 106.01 5.99 1.40e+00 5.10e-01 1.83e+01 ... (remaining 29090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 11119 17.83 - 35.66: 1024 35.66 - 53.50: 276 53.50 - 71.33: 78 71.33 - 89.16: 32 Dihedral angle restraints: 12529 sinusoidal: 4801 harmonic: 7728 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 0.98 -86.98 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -16.94 -69.06 1 1.00e+01 1.00e-02 6.17e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 30.18 62.82 1 1.00e+01 1.00e-02 5.21e+01 ... (remaining 12526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 3412 0.161 - 0.322: 1 0.322 - 0.483: 2 0.483 - 0.644: 0 0.644 - 0.805: 2 Chirality restraints: 3417 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.94e+00 ... (remaining 3414 not shown) Planarity restraints: 3719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.089 5.00e-02 4.00e+02 1.28e-01 2.62e+01 pdb=" N PRO A 521 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1098 " 0.006 2.00e-02 2.50e+03 2.30e-02 6.61e+00 pdb=" CG ASN A1098 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A1098 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN A1098 " -0.016 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 282 " 0.002 2.00e-02 2.50e+03 2.27e-02 6.45e+00 pdb=" CG ASN A 282 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 282 " -0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN A 282 " 0.026 2.00e-02 2.50e+03 pdb=" C1 NAG A1307 " -0.025 2.00e-02 2.50e+03 ... (remaining 3716 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2562 2.75 - 3.29: 19722 3.29 - 3.83: 35303 3.83 - 4.36: 42239 4.36 - 4.90: 72026 Nonbonded interactions: 171852 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.218 3.040 nonbonded pdb=" NE2 GLN C 804 " pdb=" OE1 GLN C 935 " model vdw 2.227 3.120 nonbonded pdb=" OD2 ASP C 578 " pdb=" OG1 THR C 581 " model vdw 2.233 3.040 nonbonded pdb=" NH1 ARG C 815 " pdb=" OD1 ASP C 820 " model vdw 2.235 3.120 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.269 3.040 ... (remaining 171847 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 108 or resid 116 through 130 or resid 168 throu \ gh 375 or resid 378 through 495 or resid 498 or resid 507 through 563 or (resid \ 564 and (name N or name CA or name C or name O or name CB )) or resid 565 throug \ h 570 or (resid 571 and (name N or name CA or name C or name O or name CB )) or \ resid 572 through 620 or resid 629 through 635 or resid 641 through 675 or resid \ 690 through 826 or resid 848 through 1106 or (resid 1107 and (name N or name CA \ or name C or name O or name CB )) or resid 1108 through 1138 or resid 1302 thro \ ugh 1308)) selection = (chain 'C' and (resid 27 through 404 or resid 429 through 443 or resid 451 or re \ sid 454 or resid 463 or resid 508 through 1138 or resid 1301 through 1307)) } 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=0.00 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: 9.480 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: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 20.920 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 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 0.091 21443 Z= 0.172 Angle : 0.680 18.295 29221 Z= 0.365 Chirality : 0.050 0.805 3417 Planarity : 0.005 0.128 3697 Dihedral : 16.022 89.161 7441 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.58 % Favored : 96.14 % Rotamer: Outliers : 2.03 % Allowed : 16.77 % Favored : 81.20 % 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 are not related in a simple way. whole: -0.03 (0.16), residues: 2568 helix: 2.05 (0.21), residues: 614 sheet: 0.37 (0.20), residues: 582 loop : -1.21 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.016 0.001 TYR C1067 PHE 0.036 0.001 PHE B 592 TRP 0.013 0.001 TRP A 353 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (21391) covalent geometry : angle 0.64598 / 0.36 (29095) SS BOND : bond 0.00363 / 0.19 ( 30) SS BOND : angle 1.42671 / 0.86 ( 60) hydrogen bonds : bond 0.13127 / 8.85 ( 937) hydrogen bonds : angle 7.06744 / 4.91 ( 2592) link_NAG-ASN : bond 0.00764 / 0.40 ( 22) link_NAG-ASN : angle 4.36494 / 2.75 ( 66) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6025 (pptt) cc_final: 0.5125 (pptt) REVERT: B 309 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7844 (mm-30) outliers start: 46 outliers final: 38 residues processed: 234 average time/residue: 0.4996 time to fit residues: 137.6940 Evaluate side-chains 225 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 394 ASN A 957 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 762 GLN C 81 ASN C 532 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.156497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.108212 restraints weight = 24107.744| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.77 r_work: 0.2988 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 21443 Z= 0.236 Angle : 0.712 18.881 29221 Z= 0.366 Chirality : 0.053 0.788 3417 Planarity : 0.005 0.064 3697 Dihedral : 6.206 55.882 2864 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.67 % Favored : 95.05 % Rotamer: Outliers : 3.49 % Allowed : 15.27 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.01 (0.16), residues: 2568 helix: 2.17 (0.20), residues: 616 sheet: 0.36 (0.20), residues: 580 loop : -1.25 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 815 TYR 0.019 0.002 TYR A1067 PHE 0.025 0.002 PHE B 592 TRP 0.014 0.002 TRP B 633 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 (21391) covalent geometry : angle 0.67350 / 0.36 (29095) SS BOND : bond 0.00483 / 0.29 ( 30) SS BOND : angle 1.68465 / 0.99 ( 60) hydrogen bonds : bond 0.05769 / 3.81 ( 937) hydrogen bonds : angle 6.07038 / 4.22 ( 2592) link_NAG-ASN : bond 0.00660 / 0.38 ( 22) link_NAG-ASN : angle 4.66941 / 2.93 ( 66) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 196 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1045 LYS cc_start: 0.7897 (tppp) cc_final: 0.7462 (tptt) REVERT: B 309 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8281 (mm-30) REVERT: C 338 PHE cc_start: 0.7334 (m-80) cc_final: 0.6974 (m-10) REVERT: C 357 ARG cc_start: 0.6170 (tpt170) cc_final: 0.5738 (tpt170) REVERT: C 467 ASP cc_start: 0.5602 (t70) cc_final: 0.4876 (t0) REVERT: C 607 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8322 (mt0) REVERT: C 759 PHE cc_start: 0.6978 (m-80) cc_final: 0.6673 (t80) REVERT: C 856 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8207 (mtpp) REVERT: C 973 ILE cc_start: 0.7159 (OUTLIER) cc_final: 0.6764 (tp) outliers start: 79 outliers final: 45 residues processed: 254 average time/residue: 0.5304 time to fit residues: 158.2296 Evaluate side-chains 229 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 142 optimal weight: 0.8980 chunk 124 optimal weight: 0.2980 chunk 137 optimal weight: 0.0870 chunk 212 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN B 30 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 675 GLN C 804 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.159749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112185 restraints weight = 24129.097| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.72 r_work: 0.3063 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21443 Z= 0.118 Angle : 0.580 17.918 29221 Z= 0.296 Chirality : 0.048 0.619 3417 Planarity : 0.004 0.046 3697 Dihedral : 5.352 51.897 2845 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.35 % Favored : 96.38 % Rotamer: Outliers : 2.87 % Allowed : 16.11 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.16), residues: 2568 helix: 2.47 (0.20), residues: 612 sheet: 0.46 (0.21), residues: 566 loop : -1.08 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.016 0.001 TYR C1067 PHE 0.028 0.001 PHE B 592 TRP 0.011 0.001 TRP C 633 HIS 0.002 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (21391) covalent geometry : angle 0.54579 / 0.29 (29095) SS BOND : bond 0.00296 / 0.18 ( 30) SS BOND : angle 1.27097 / 0.76 ( 60) hydrogen bonds : bond 0.04364 / 2.86 ( 937) hydrogen bonds : angle 5.59917 / 3.91 ( 2592) link_NAG-ASN : bond 0.00641 / 0.33 ( 22) link_NAG-ASN : angle 4.03726 / 2.49 ( 66) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5329 (OUTLIER) cc_final: 0.5057 (mt) REVERT: A 237 ARG cc_start: 0.7276 (mtp180) cc_final: 0.7044 (mtp85) REVERT: A 973 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8344 (pp) REVERT: A 1117 THR cc_start: 0.7899 (m) cc_final: 0.7623 (p) REVERT: B 309 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8186 (mm-30) REVERT: B 965 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7993 (mt0) REVERT: C 338 PHE cc_start: 0.7392 (m-80) cc_final: 0.7021 (m-10) REVERT: C 467 ASP cc_start: 0.5597 (t70) cc_final: 0.5035 (p0) REVERT: C 607 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: C 759 PHE cc_start: 0.6777 (m-80) cc_final: 0.6414 (t80) REVERT: C 973 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6611 (tp) REVERT: H 96 LYS cc_start: 0.6428 (OUTLIER) cc_final: 0.5977 (mptt) outliers start: 65 outliers final: 35 residues processed: 236 average time/residue: 0.4862 time to fit residues: 136.5172 Evaluate side-chains 222 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 145 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 42 optimal weight: 0.0970 chunk 213 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A 957 GLN B 703 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.158396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.108887 restraints weight = 24104.504| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.62 r_work: 0.3040 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 21443 Z= 0.164 Angle : 0.618 17.832 29221 Z= 0.316 Chirality : 0.049 0.678 3417 Planarity : 0.004 0.046 3697 Dihedral : 5.348 54.767 2837 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.48 % Favored : 95.25 % Rotamer: Outliers : 3.22 % Allowed : 16.11 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.16), residues: 2568 helix: 2.49 (0.20), residues: 603 sheet: 0.45 (0.20), residues: 578 loop : -1.12 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 646 TYR 0.018 0.002 TYR B1067 PHE 0.027 0.001 PHE B 592 TRP 0.010 0.002 TRP C 633 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (21391) covalent geometry : angle 0.58252 / 0.31 (29095) SS BOND : bond 0.00386 / 0.22 ( 30) SS BOND : angle 1.43083 / 0.85 ( 60) hydrogen bonds : bond 0.04920 / 3.22 ( 937) hydrogen bonds : angle 5.69029 / 3.96 ( 2592) link_NAG-ASN : bond 0.00621 / 0.33 ( 22) link_NAG-ASN : angle 4.21304 / 2.58 ( 66) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 188 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5357 (OUTLIER) cc_final: 0.5076 (mt) REVERT: A 237 ARG cc_start: 0.7274 (mtp180) cc_final: 0.7026 (mtp85) REVERT: A 973 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8379 (pp) REVERT: A 1107 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7983 (mpt180) REVERT: A 1117 THR cc_start: 0.7939 (m) cc_final: 0.7682 (p) REVERT: B 309 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8177 (mm-30) REVERT: C 338 PHE cc_start: 0.7419 (m-80) cc_final: 0.7027 (m-10) REVERT: C 467 ASP cc_start: 0.5553 (t70) cc_final: 0.5042 (p0) REVERT: C 607 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: C 759 PHE cc_start: 0.6902 (m-80) cc_final: 0.6609 (t80) REVERT: C 856 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8180 (mtpp) REVERT: C 973 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6786 (tp) REVERT: C 1113 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7830 (mm110) outliers start: 73 outliers final: 44 residues processed: 241 average time/residue: 0.5020 time to fit residues: 143.1548 Evaluate side-chains 229 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 259 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 229 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A 957 GLN B 87 ASN C 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.158831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.110225 restraints weight = 24009.484| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.76 r_work: 0.3033 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21443 Z= 0.147 Angle : 0.595 17.657 29221 Z= 0.304 Chirality : 0.049 0.644 3417 Planarity : 0.004 0.046 3697 Dihedral : 5.255 59.114 2837 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.62 % Favored : 96.11 % Rotamer: Outliers : 3.44 % Allowed : 16.20 % Favored : 80.36 % 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 are not related in a simple way. whole: 0.26 (0.16), residues: 2568 helix: 2.51 (0.20), residues: 606 sheet: 0.44 (0.21), residues: 578 loop : -1.07 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.018 0.001 TYR B1067 PHE 0.031 0.001 PHE B 592 TRP 0.011 0.001 TRP C 633 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (21391) covalent geometry : angle 0.55959 / 0.30 (29095) SS BOND : bond 0.00340 / 0.19 ( 30) SS BOND : angle 1.31616 / 0.78 ( 60) hydrogen bonds : bond 0.04636 / 3.03 ( 937) hydrogen bonds : angle 5.57847 / 3.88 ( 2592) link_NAG-ASN : bond 0.00646 / 0.34 ( 22) link_NAG-ASN : angle 4.14314 / 2.55 ( 66) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 179 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5411 (OUTLIER) cc_final: 0.5117 (mt) REVERT: A 237 ARG cc_start: 0.7268 (mtp180) cc_final: 0.7015 (mtp85) REVERT: A 1117 THR cc_start: 0.7923 (m) cc_final: 0.7688 (p) REVERT: B 309 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8260 (mm-30) REVERT: B 965 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8056 (mt0) REVERT: C 338 PHE cc_start: 0.7399 (m-80) cc_final: 0.7009 (m-10) REVERT: C 357 ARG cc_start: 0.7504 (ttt-90) cc_final: 0.7268 (tpt170) REVERT: C 467 ASP cc_start: 0.5554 (t70) cc_final: 0.5065 (p0) REVERT: C 607 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8327 (mt0) REVERT: C 759 PHE cc_start: 0.6907 (m-80) cc_final: 0.6534 (t80) REVERT: C 1113 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7874 (mm110) REVERT: H 34 MET cc_start: 0.3717 (mmm) cc_final: 0.3482 (mmm) outliers start: 78 outliers final: 43 residues processed: 239 average time/residue: 0.4775 time to fit residues: 135.7225 Evaluate side-chains 225 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 178 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 165 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 198 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A 394 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.106961 restraints weight = 23875.275| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.64 r_work: 0.3014 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 21443 Z= 0.259 Angle : 0.712 17.926 29221 Z= 0.365 Chirality : 0.053 0.720 3417 Planarity : 0.005 0.052 3697 Dihedral : 5.638 51.807 2834 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.06 % Favored : 94.70 % Rotamer: Outliers : 3.53 % Allowed : 16.86 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: 0.05 (0.16), residues: 2568 helix: 2.23 (0.20), residues: 609 sheet: 0.29 (0.20), residues: 600 loop : -1.17 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 357 TYR 0.018 0.002 TYR A1067 PHE 0.028 0.002 PHE B 592 TRP 0.013 0.003 TRP B 633 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.26 (21391) covalent geometry : angle 0.67538 / 0.36 (29095) SS BOND : bond 0.00618 / 0.41 ( 30) SS BOND : angle 1.64241 / 0.98 ( 60) hydrogen bonds : bond 0.05733 / 3.78 ( 937) hydrogen bonds : angle 5.94909 / 4.12 ( 2592) link_NAG-ASN : bond 0.00704 / 0.40 ( 22) link_NAG-ASN : angle 4.54017 / 2.81 ( 66) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 196 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5420 (OUTLIER) cc_final: 0.5172 (mt) REVERT: A 916 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8504 (tt) REVERT: A 973 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8426 (pp) REVERT: A 1107 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8078 (mtt180) REVERT: A 1117 THR cc_start: 0.7955 (m) cc_final: 0.7743 (p) REVERT: B 740 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8595 (tpt) REVERT: C 101 ILE cc_start: 0.6114 (OUTLIER) cc_final: 0.5906 (tp) REVERT: C 236 THR cc_start: 0.7172 (m) cc_final: 0.6929 (t) REVERT: C 338 PHE cc_start: 0.7354 (m-80) cc_final: 0.6954 (m-10) REVERT: C 357 ARG cc_start: 0.7563 (ttt-90) cc_final: 0.7286 (ttt180) REVERT: C 467 ASP cc_start: 0.5557 (t70) cc_final: 0.5099 (p0) REVERT: C 607 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8303 (mt0) REVERT: C 759 PHE cc_start: 0.7143 (m-80) cc_final: 0.6832 (t80) REVERT: C 856 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8817 (mmtp) REVERT: C 1113 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7642 (mm110) outliers start: 80 outliers final: 53 residues processed: 258 average time/residue: 0.4804 time to fit residues: 147.0788 Evaluate side-chains 247 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 185 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 233 optimal weight: 1.9990 chunk 229 optimal weight: 0.4980 chunk 152 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 751 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN C 239 GLN C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.158010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.108553 restraints weight = 23999.838| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.62 r_work: 0.3047 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 21443 Z= 0.168 Angle : 0.631 17.139 29221 Z= 0.322 Chirality : 0.049 0.644 3417 Planarity : 0.005 0.055 3697 Dihedral : 5.363 50.803 2834 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.13 % Favored : 95.64 % Rotamer: Outliers : 3.18 % Allowed : 17.70 % Favored : 79.13 % 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 are not related in a simple way. whole: 0.15 (0.16), residues: 2568 helix: 2.34 (0.20), residues: 621 sheet: 0.34 (0.20), residues: 590 loop : -1.13 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.018 0.002 TYR A1067 PHE 0.029 0.002 PHE B 592 TRP 0.013 0.002 TRP A 353 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (21391) covalent geometry : angle 0.59190 / 0.31 (29095) SS BOND : bond 0.00452 / 0.29 ( 30) SS BOND : angle 1.39715 / 0.84 ( 60) hydrogen bonds : bond 0.04914 / 3.22 ( 937) hydrogen bonds : angle 5.71695 / 3.97 ( 2592) link_NAG-ASN : bond 0.00622 / 0.33 ( 22) link_NAG-ASN : angle 4.45263 / 2.77 ( 66) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 192 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5395 (OUTLIER) cc_final: 0.5102 (mt) REVERT: A 237 ARG cc_start: 0.7232 (mtp180) cc_final: 0.6954 (mtp85) REVERT: A 392 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: A 973 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8453 (pp) REVERT: B 309 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8193 (mm-30) REVERT: C 206 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7994 (tttp) REVERT: C 338 PHE cc_start: 0.7407 (m-80) cc_final: 0.6988 (m-10) REVERT: C 467 ASP cc_start: 0.5598 (t70) cc_final: 0.5113 (p0) REVERT: C 607 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: C 759 PHE cc_start: 0.6965 (m-80) cc_final: 0.6625 (t80) REVERT: C 856 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8817 (mmtp) REVERT: C 1113 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7652 (mm110) outliers start: 72 outliers final: 49 residues processed: 249 average time/residue: 0.5007 time to fit residues: 147.4683 Evaluate side-chains 235 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 199 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 108 optimal weight: 0.0470 chunk 236 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 354 ASN A 394 ASN A 751 ASN A 957 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.158534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.110672 restraints weight = 23898.160| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.77 r_work: 0.3023 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 21443 Z= 0.150 Angle : 0.606 17.907 29221 Z= 0.309 Chirality : 0.049 0.673 3417 Planarity : 0.004 0.052 3697 Dihedral : 5.189 50.532 2834 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.48 % Favored : 95.29 % Rotamer: Outliers : 2.91 % Allowed : 17.83 % Favored : 79.26 % 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 are not related in a simple way. whole: 0.23 (0.16), residues: 2568 helix: 2.45 (0.20), residues: 617 sheet: 0.39 (0.20), residues: 590 loop : -1.10 (0.16), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 646 TYR 0.017 0.002 TYR B1067 PHE 0.029 0.001 PHE B 592 TRP 0.013 0.002 TRP A 353 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (21391) covalent geometry : angle 0.56956 / 0.30 (29095) SS BOND : bond 0.00405 / 0.25 ( 30) SS BOND : angle 1.23582 / 0.76 ( 60) hydrogen bonds : bond 0.04669 / 3.06 ( 937) hydrogen bonds : angle 5.60327 / 3.90 ( 2592) link_NAG-ASN : bond 0.00611 / 0.32 ( 22) link_NAG-ASN : angle 4.27547 / 2.65 ( 66) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 193 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5332 (OUTLIER) cc_final: 0.5027 (mt) REVERT: A 237 ARG cc_start: 0.7249 (mtp180) cc_final: 0.6975 (mtp85) REVERT: A 392 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.7549 (m-80) REVERT: B 309 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8264 (mm-30) REVERT: B 740 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8441 (tpt) REVERT: C 206 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8026 (tttp) REVERT: C 236 THR cc_start: 0.7087 (m) cc_final: 0.6835 (t) REVERT: C 338 PHE cc_start: 0.7345 (m-80) cc_final: 0.6903 (m-10) REVERT: C 357 ARG cc_start: 0.7516 (ttt-90) cc_final: 0.7172 (tmt170) REVERT: C 467 ASP cc_start: 0.5554 (t70) cc_final: 0.5140 (p0) REVERT: C 607 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8312 (mt0) REVERT: C 759 PHE cc_start: 0.6891 (m-80) cc_final: 0.6512 (t80) REVERT: C 856 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8829 (mmtp) REVERT: C 1113 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7845 (mm110) outliers start: 66 outliers final: 46 residues processed: 244 average time/residue: 0.4826 time to fit residues: 139.3634 Evaluate side-chains 235 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 182 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain H residue 99 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 92 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 245 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 216 optimal weight: 0.0270 chunk 8 optimal weight: 0.9980 chunk 228 optimal weight: 0.7980 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN A 394 ASN A 751 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.159343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.111844 restraints weight = 23910.078| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.75 r_work: 0.3038 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21443 Z= 0.129 Angle : 0.581 16.830 29221 Z= 0.296 Chirality : 0.048 0.648 3417 Planarity : 0.004 0.053 3697 Dihedral : 4.893 48.409 2832 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.66 % Favored : 96.11 % Rotamer: Outliers : 2.47 % Allowed : 18.62 % Favored : 78.91 % 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 are not related in a simple way. whole: 0.30 (0.16), residues: 2568 helix: 2.54 (0.20), residues: 621 sheet: 0.44 (0.20), residues: 587 loop : -1.09 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 646 TYR 0.017 0.001 TYR B1067 PHE 0.029 0.001 PHE B 592 TRP 0.014 0.001 TRP A 353 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (21391) covalent geometry : angle 0.54426 / 0.29 (29095) SS BOND : bond 0.00339 / 0.19 ( 30) SS BOND : angle 1.31682 / 0.76 ( 60) hydrogen bonds : bond 0.04396 / 2.86 ( 937) hydrogen bonds : angle 5.48352 / 3.83 ( 2592) link_NAG-ASN : bond 0.00607 / 0.31 ( 22) link_NAG-ASN : angle 4.15932 / 2.56 ( 66) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 183 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5351 (OUTLIER) cc_final: 0.5055 (mt) REVERT: A 237 ARG cc_start: 0.7220 (mtp180) cc_final: 0.6975 (mtp85) REVERT: A 392 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: B 309 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8251 (mm-30) REVERT: C 101 ILE cc_start: 0.6182 (OUTLIER) cc_final: 0.5926 (tp) REVERT: C 206 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8004 (tttp) REVERT: C 241 LEU cc_start: 0.6613 (mt) cc_final: 0.6175 (pp) REVERT: C 338 PHE cc_start: 0.7419 (m-80) cc_final: 0.6964 (m-10) REVERT: C 357 ARG cc_start: 0.7442 (ttt-90) cc_final: 0.7101 (tmt170) REVERT: C 467 ASP cc_start: 0.5520 (t70) cc_final: 0.5180 (p0) REVERT: C 607 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: C 740 MET cc_start: 0.8434 (ttt) cc_final: 0.8232 (ttm) REVERT: C 856 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8812 (mmtp) REVERT: C 1113 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7914 (mm110) REVERT: H 34 MET cc_start: 0.4051 (mmm) cc_final: 0.3743 (mmm) outliers start: 56 outliers final: 41 residues processed: 227 average time/residue: 0.4177 time to fit residues: 113.1045 Evaluate side-chains 225 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 134 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 180 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 264 optimal weight: 8.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN A 394 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.110239 restraints weight = 24054.946| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.82 r_work: 0.3029 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21443 Z= 0.134 Angle : 0.584 16.785 29221 Z= 0.298 Chirality : 0.048 0.632 3417 Planarity : 0.004 0.053 3697 Dihedral : 4.749 47.036 2829 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.24 % Favored : 95.52 % Rotamer: Outliers : 2.25 % Allowed : 18.84 % Favored : 78.91 % 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 are not related in a simple way. whole: 0.31 (0.16), residues: 2568 helix: 2.56 (0.20), residues: 618 sheet: 0.46 (0.20), residues: 587 loop : -1.08 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.019 0.001 TYR B 904 PHE 0.026 0.001 PHE B 592 TRP 0.015 0.001 TRP A 353 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (21391) covalent geometry : angle 0.54876 / 0.29 (29095) SS BOND : bond 0.00337 / 0.19 ( 30) SS BOND : angle 1.33869 / 0.79 ( 60) hydrogen bonds : bond 0.04470 / 2.91 ( 937) hydrogen bonds : angle 5.48883 / 3.83 ( 2592) link_NAG-ASN : bond 0.00611 / 0.32 ( 22) link_NAG-ASN : angle 4.06526 / 2.51 ( 66) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5399 (OUTLIER) cc_final: 0.5071 (mt) REVERT: A 237 ARG cc_start: 0.7237 (mtp180) cc_final: 0.6993 (mtp85) REVERT: B 309 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8285 (mm-30) REVERT: B 740 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8422 (tpt) REVERT: C 101 ILE cc_start: 0.6219 (OUTLIER) cc_final: 0.5933 (tp) REVERT: C 118 LEU cc_start: 0.8142 (tp) cc_final: 0.7805 (tm) REVERT: C 206 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8029 (tttp) REVERT: C 241 LEU cc_start: 0.6681 (mt) cc_final: 0.6287 (pp) REVERT: C 357 ARG cc_start: 0.7441 (ttt-90) cc_final: 0.7102 (tmt170) REVERT: C 467 ASP cc_start: 0.5536 (t70) cc_final: 0.5217 (p0) REVERT: C 607 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8325 (mt0) REVERT: C 740 MET cc_start: 0.8430 (ttt) cc_final: 0.8223 (ttm) REVERT: C 759 PHE cc_start: 0.6766 (m-80) cc_final: 0.6276 (t80) REVERT: C 856 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8826 (mmtp) REVERT: C 1113 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7925 (mm110) REVERT: H 34 MET cc_start: 0.4028 (mmm) cc_final: 0.3736 (mmm) outliers start: 51 outliers final: 40 residues processed: 225 average time/residue: 0.4482 time to fit residues: 119.6979 Evaluate side-chains 223 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 153 optimal weight: 0.0170 chunk 169 optimal weight: 0.8980 chunk 221 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 251 optimal weight: 0.5980 chunk 213 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN A 394 ASN A 751 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.159924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.111894 restraints weight = 24043.546| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.81 r_work: 0.3042 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21443 Z= 0.121 Angle : 0.562 16.362 29221 Z= 0.287 Chirality : 0.047 0.603 3417 Planarity : 0.004 0.053 3697 Dihedral : 4.559 43.610 2827 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.31 % Favored : 96.46 % Rotamer: Outliers : 2.38 % Allowed : 18.76 % Favored : 78.86 % 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 are not related in a simple way. whole: 0.36 (0.16), residues: 2568 helix: 2.60 (0.20), residues: 624 sheet: 0.46 (0.20), residues: 600 loop : -1.06 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.021 0.001 TYR B 904 PHE 0.028 0.001 PHE B 592 TRP 0.018 0.001 TRP A 353 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (21391) covalent geometry : angle 0.52908 / 0.28 (29095) SS BOND : bond 0.00312 / 0.17 ( 30) SS BOND : angle 1.18439 / 0.71 ( 60) hydrogen bonds : bond 0.04212 / 2.74 ( 937) hydrogen bonds : angle 5.37175 / 3.75 ( 2592) link_NAG-ASN : bond 0.00603 / 0.31 ( 22) link_NAG-ASN : angle 3.89396 / 2.40 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8850.50 seconds wall clock time: 151 minutes 25.17 seconds (9085.17 seconds total)