Starting phenix.real_space_refine on Sun Aug 24 15:54:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3m_34469/08_2025/8h3m_34469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3m_34469/08_2025/8h3m_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 { model { file = "/net/cci-nas-00/data/ceres_data/8h3m_34469/08_2025/8h3m_34469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3m_34469/08_2025/8h3m_34469.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h3m_34469/08_2025/8h3m_34469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3m_34469/08_2025/8h3m_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 27 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 dihedrals: 18 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 4.61, 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: 1.71 Conformation dependent library (CDL) restraints added in 902.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.56 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: 4.05 Time building geometry restraints manager: 2.09 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 - 20.74: 11771 20.74 - 41.48: 933 41.48 - 62.22: 224 62.22 - 82.96: 48 82.96 - 103.70: 15 Dihedral angle restraints: 12991 sinusoidal: 5263 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 12988 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: 8.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.310 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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 : 16.222 103.698 7903 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 aren 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 covalent geometry : bond 0.00358 (21391) covalent geometry : angle 0.64598 (29095) SS BOND : bond 0.00363 ( 30) SS BOND : angle 1.42671 ( 60) hydrogen bonds : bond 0.13127 ( 937) hydrogen bonds : angle 7.06744 ( 2592) link_NAG-ASN : bond 0.00764 ( 22) link_NAG-ASN : angle 4.36494 ( 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 : 0.598 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: 0.4747 time to fit residues: 130.0780 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 : 0.841 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3850 r_free = 0.3850 target = 0.156518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.108406 restraints weight = 24115.084| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.66 r_work: 0.3016 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 21443 Z= 0.235 Angle : 0.712 18.463 29221 Z= 0.366 Chirality : 0.053 0.744 3417 Planarity : 0.005 0.065 3697 Dihedral : 7.832 68.021 3326 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.71 % Favored : 95.02 % 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 aren not related in a simple way. whole: -0.01 (0.16), residues: 2568 helix: 2.18 (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 covalent geometry : bond 0.00539 (21391) covalent geometry : angle 0.67453 (29095) SS BOND : bond 0.00480 ( 30) SS BOND : angle 1.67903 ( 60) hydrogen bonds : bond 0.05776 ( 937) hydrogen bonds : angle 6.07410 ( 2592) link_NAG-ASN : bond 0.00662 ( 22) link_NAG-ASN : angle 4.63495 ( 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 276 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 197 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1045 LYS cc_start: 0.7858 (tppp) cc_final: 0.7472 (tptt) REVERT: B 309 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8213 (mm-30) REVERT: C 338 PHE cc_start: 0.7337 (m-80) cc_final: 0.6978 (m-10) REVERT: C 357 ARG cc_start: 0.6117 (tpt170) cc_final: 0.5689 (tpt170) REVERT: C 467 ASP cc_start: 0.5559 (t70) cc_final: 0.4853 (t0) REVERT: C 607 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8285 (mt0) REVERT: C 759 PHE cc_start: 0.6940 (m-80) cc_final: 0.6666 (t80) REVERT: C 856 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8187 (mtpp) REVERT: C 973 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6767 (tp) outliers start: 79 outliers final: 45 residues processed: 255 average time/residue: 0.5016 time to fit residues: 150.2120 Evaluate side-chains 228 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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: 0.9980 chunk 124 optimal weight: 0.6980 chunk 137 optimal weight: 0.0670 chunk 212 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 147 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 30 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3881 r_free = 0.3881 target = 0.159810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.111707 restraints weight = 24136.125| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.76 r_work: 0.3053 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21443 Z= 0.122 Angle : 0.578 17.468 29221 Z= 0.295 Chirality : 0.048 0.678 3417 Planarity : 0.004 0.046 3697 Dihedral : 6.127 59.511 3307 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.19 % Favored : 96.53 % Rotamer: Outliers : 2.91 % Allowed : 15.84 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.16), residues: 2568 helix: 2.50 (0.20), residues: 617 sheet: 0.47 (0.21), residues: 572 loop : -1.10 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 646 TYR 0.016 0.001 TYR B1067 PHE 0.028 0.001 PHE B 592 TRP 0.011 0.001 TRP C 633 HIS 0.002 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00261 (21391) covalent geometry : angle 0.54319 (29095) SS BOND : bond 0.00264 ( 30) SS BOND : angle 1.25709 ( 60) hydrogen bonds : bond 0.04328 ( 937) hydrogen bonds : angle 5.55601 ( 2592) link_NAG-ASN : bond 0.00613 ( 22) link_NAG-ASN : angle 4.02268 ( 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 258 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 192 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5295 (OUTLIER) cc_final: 0.5013 (mt) REVERT: A 237 ARG cc_start: 0.7264 (mtp180) cc_final: 0.7040 (mtp85) REVERT: A 528 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7773 (mmtm) REVERT: A 1117 THR cc_start: 0.7896 (m) cc_final: 0.7620 (p) REVERT: B 309 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8197 (mm-30) REVERT: B 965 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8003 (mt0) REVERT: C 338 PHE cc_start: 0.7399 (m-80) cc_final: 0.7026 (m-10) REVERT: C 467 ASP cc_start: 0.5595 (t70) cc_final: 0.5062 (p0) REVERT: C 607 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8298 (mt0) REVERT: C 759 PHE cc_start: 0.6787 (m-80) cc_final: 0.6390 (t80) REVERT: C 973 ILE cc_start: 0.7032 (OUTLIER) cc_final: 0.6593 (tp) REVERT: H 96 LYS cc_start: 0.6378 (OUTLIER) cc_final: 0.5929 (mptt) outliers start: 66 outliers final: 34 residues processed: 239 average time/residue: 0.5005 time to fit residues: 141.3254 Evaluate side-chains 219 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 528 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 616 ASN 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 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 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 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: 3.9990 chunk 42 optimal weight: 0.0870 chunk 213 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.157482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108105 restraints weight = 24064.765| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.76 r_work: 0.3012 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 21443 Z= 0.207 Angle : 0.664 17.862 29221 Z= 0.340 Chirality : 0.052 0.800 3417 Planarity : 0.005 0.050 3697 Dihedral : 6.320 58.143 3298 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.56 % Favored : 95.17 % Rotamer: Outliers : 3.53 % Allowed : 15.98 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.16), residues: 2568 helix: 2.37 (0.20), residues: 605 sheet: 0.39 (0.20), residues: 599 loop : -1.15 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 815 TYR 0.019 0.002 TYR B1067 PHE 0.027 0.002 PHE B 592 TRP 0.011 0.002 TRP B 633 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00473 (21391) covalent geometry : angle 0.62779 (29095) SS BOND : bond 0.00453 ( 30) SS BOND : angle 1.54794 ( 60) hydrogen bonds : bond 0.05366 ( 937) hydrogen bonds : angle 5.83857 ( 2592) link_NAG-ASN : bond 0.00612 ( 22) link_NAG-ASN : angle 4.37388 ( 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 270 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 190 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5401 (OUTLIER) cc_final: 0.5134 (mt) REVERT: A 973 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8454 (pp) REVERT: A 1107 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8028 (mpt180) REVERT: A 1117 THR cc_start: 0.7957 (m) cc_final: 0.7703 (p) REVERT: B 309 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8233 (mm-30) REVERT: B 820 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: C 338 PHE cc_start: 0.7410 (m-80) cc_final: 0.7041 (m-10) REVERT: C 467 ASP cc_start: 0.5528 (t70) cc_final: 0.5049 (p0) REVERT: C 607 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8317 (mt0) REVERT: C 759 PHE cc_start: 0.7015 (m-80) cc_final: 0.6721 (t80) REVERT: C 856 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8202 (mtpp) REVERT: C 973 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.6849 (tp) REVERT: C 1113 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7687 (mm110) outliers start: 80 outliers final: 46 residues processed: 250 average time/residue: 0.4750 time to fit residues: 139.9637 Evaluate side-chains 231 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 177 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU 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 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 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 820 ASP 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 335 LEU Chi-restraints excluded: chain C residue 345 THR 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 761 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 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: 0.7980 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.158168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.109414 restraints weight = 23944.735| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.74 r_work: 0.3030 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.0956 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 : 0.620 16.831 29221 Z= 0.318 Chirality : 0.050 0.732 3417 Planarity : 0.004 0.049 3697 Dihedral : 6.062 57.900 3298 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.89 % Favored : 95.83 % Rotamer: Outliers : 3.44 % Allowed : 16.73 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.16), residues: 2568 helix: 2.42 (0.20), residues: 606 sheet: 0.38 (0.20), residues: 588 loop : -1.10 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.018 0.002 TYR B1067 PHE 0.030 0.002 PHE B 592 TRP 0.011 0.002 TRP C 633 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00377 (21391) covalent geometry : angle 0.58446 (29095) SS BOND : bond 0.00380 ( 30) SS BOND : angle 1.41667 ( 60) hydrogen bonds : bond 0.04898 ( 937) hydrogen bonds : angle 5.69608 ( 2592) link_NAG-ASN : bond 0.00637 ( 22) link_NAG-ASN : angle 4.23630 ( 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 258 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 180 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.5177 (mt) REVERT: A 1107 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7999 (mpt180) REVERT: A 1117 THR cc_start: 0.7947 (m) cc_final: 0.7722 (p) REVERT: B 309 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8241 (mm-30) REVERT: C 338 PHE cc_start: 0.7390 (m-80) cc_final: 0.7012 (m-10) REVERT: C 357 ARG cc_start: 0.7505 (ttt-90) cc_final: 0.7221 (ttt180) REVERT: C 467 ASP cc_start: 0.5583 (t70) cc_final: 0.5112 (p0) REVERT: C 607 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8312 (mt0) REVERT: C 759 PHE cc_start: 0.6942 (m-80) cc_final: 0.6612 (t80) REVERT: C 973 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6743 (tp) REVERT: C 1113 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7689 (mm110) outliers start: 78 outliers final: 45 residues processed: 240 average time/residue: 0.5100 time to fit residues: 144.7595 Evaluate side-chains 230 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU 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 1058 HIS Chi-restraints excluded: chain A residue 1107 ARG 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 126 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 326 ILE 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 205 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU 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 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 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: 1.9990 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 394 ASN ** A 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.157100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107301 restraints weight = 23874.271| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.75 r_work: 0.3011 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 21443 Z= 0.220 Angle : 0.674 17.476 29221 Z= 0.346 Chirality : 0.052 0.733 3417 Planarity : 0.005 0.052 3697 Dihedral : 6.212 56.899 3297 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.87 % Favored : 94.90 % Rotamer: Outliers : 3.49 % Allowed : 17.17 % Favored : 79.35 % 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 aren not related in a simple way. whole: 0.08 (0.16), residues: 2568 helix: 2.28 (0.20), residues: 609 sheet: 0.31 (0.20), residues: 600 loop : -1.16 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 357 TYR 0.019 0.002 TYR B1067 PHE 0.028 0.002 PHE B 592 TRP 0.013 0.002 TRP B 633 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00503 (21391) covalent geometry : angle 0.63841 (29095) SS BOND : bond 0.00576 ( 30) SS BOND : angle 1.56064 ( 60) hydrogen bonds : bond 0.05429 ( 937) hydrogen bonds : angle 5.86461 ( 2592) link_NAG-ASN : bond 0.00641 ( 22) link_NAG-ASN : angle 4.39447 ( 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 270 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 191 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5489 (OUTLIER) cc_final: 0.5202 (mt) REVERT: A 1107 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8050 (mtt180) REVERT: A 1117 THR cc_start: 0.7917 (m) cc_final: 0.7711 (p) REVERT: B 309 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8249 (mm-30) REVERT: B 740 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8603 (tpt) REVERT: C 101 ILE cc_start: 0.6112 (OUTLIER) cc_final: 0.5868 (tp) REVERT: C 236 THR cc_start: 0.7128 (m) cc_final: 0.6869 (t) REVERT: C 338 PHE cc_start: 0.7367 (m-80) cc_final: 0.6955 (m-10) REVERT: C 467 ASP cc_start: 0.5534 (t70) cc_final: 0.5102 (p0) REVERT: C 607 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8316 (mt0) REVERT: C 759 PHE cc_start: 0.7098 (m-80) cc_final: 0.6762 (t80) REVERT: C 856 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8829 (mmtp) REVERT: C 973 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6814 (tp) REVERT: C 1113 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7653 (mm110) outliers start: 79 outliers final: 50 residues processed: 252 average time/residue: 0.5049 time to fit residues: 150.6114 Evaluate side-chains 236 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU 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 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 916 LEU 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 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 101 ILE Chi-restraints excluded: chain C residue 205 SER 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 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 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 973 ILE 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: 3.9990 chunk 25 optimal weight: 0.9980 chunk 62 optimal weight: 0.0040 chunk 233 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 110 optimal weight: 0.2980 chunk 174 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 751 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3861 r_free = 0.3861 target = 0.158269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.108952 restraints weight = 23984.817| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.76 r_work: 0.3016 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 21443 Z= 0.156 Angle : 0.613 16.829 29221 Z= 0.314 Chirality : 0.050 0.750 3417 Planarity : 0.004 0.051 3697 Dihedral : 5.912 53.403 3297 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.93 % Favored : 95.83 % Rotamer: Outliers : 3.18 % Allowed : 17.61 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.16), residues: 2568 helix: 2.38 (0.20), residues: 620 sheet: 0.36 (0.20), residues: 599 loop : -1.12 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.017 0.002 TYR A1067 PHE 0.031 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 covalent geometry : bond 0.00349 (21391) covalent geometry : angle 0.57804 (29095) SS BOND : bond 0.00444 ( 30) SS BOND : angle 1.29973 ( 60) hydrogen bonds : bond 0.04790 ( 937) hydrogen bonds : angle 5.67566 ( 2592) link_NAG-ASN : bond 0.00618 ( 22) link_NAG-ASN : angle 4.21034 ( 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 258 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 186 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5403 (OUTLIER) cc_final: 0.5100 (mt) REVERT: A 237 ARG cc_start: 0.7263 (mtp180) cc_final: 0.6978 (mtp85) REVERT: A 392 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: A 1117 THR cc_start: 0.7941 (m) cc_final: 0.7730 (p) REVERT: B 309 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8266 (mm-30) REVERT: B 740 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8486 (tpt) REVERT: B 820 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: C 101 ILE cc_start: 0.6100 (OUTLIER) cc_final: 0.5826 (tp) REVERT: C 338 PHE cc_start: 0.7389 (m-80) cc_final: 0.6967 (m-10) REVERT: C 357 ARG cc_start: 0.7465 (ttt-90) cc_final: 0.7119 (tmt170) REVERT: C 467 ASP cc_start: 0.5543 (t70) cc_final: 0.5164 (p0) REVERT: C 607 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8320 (mt0) REVERT: C 759 PHE cc_start: 0.6974 (m-80) cc_final: 0.6579 (t80) REVERT: C 856 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8832 (mmtp) REVERT: C 1113 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7679 (mm110) outliers start: 72 outliers final: 47 residues processed: 242 average time/residue: 0.4967 time to fit residues: 141.9747 Evaluate side-chains 233 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU 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 1058 HIS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1133 VAL 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 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 820 ASP 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 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 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 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: 0.8980 chunk 91 optimal weight: 9.9990 chunk 108 optimal weight: 0.4980 chunk 236 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 201 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.159055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.109918 restraints weight = 23875.073| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.71 r_work: 0.3047 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21443 Z= 0.137 Angle : 0.587 16.131 29221 Z= 0.299 Chirality : 0.048 0.672 3417 Planarity : 0.004 0.052 3697 Dihedral : 5.672 56.778 3297 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.28 % Favored : 95.48 % Rotamer: Outliers : 3.09 % Allowed : 17.87 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.16), residues: 2568 helix: 2.47 (0.20), residues: 618 sheet: 0.42 (0.20), residues: 590 loop : -1.06 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.018 0.001 TYR B1067 PHE 0.033 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 covalent geometry : bond 0.00304 (21391) covalent geometry : angle 0.55275 (29095) SS BOND : bond 0.00396 ( 30) SS BOND : angle 1.19513 ( 60) hydrogen bonds : bond 0.04482 ( 937) hydrogen bonds : angle 5.51530 ( 2592) link_NAG-ASN : bond 0.00562 ( 22) link_NAG-ASN : angle 4.04799 ( 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 256 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 186 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5406 (OUTLIER) cc_final: 0.5107 (mt) REVERT: A 237 ARG cc_start: 0.7241 (mtp180) cc_final: 0.6985 (mtp85) REVERT: A 392 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.7697 (m-80) REVERT: A 1117 THR cc_start: 0.7913 (m) cc_final: 0.7703 (p) REVERT: B 309 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8233 (mm-30) REVERT: B 740 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8453 (tpt) REVERT: C 101 ILE cc_start: 0.6133 (OUTLIER) cc_final: 0.5865 (tp) REVERT: C 118 LEU cc_start: 0.8157 (tp) cc_final: 0.7818 (tm) REVERT: C 241 LEU cc_start: 0.6786 (mt) cc_final: 0.6340 (pp) REVERT: C 338 PHE cc_start: 0.7363 (m-80) cc_final: 0.6917 (m-10) REVERT: C 357 ARG cc_start: 0.7393 (ttt-90) cc_final: 0.7084 (tmt170) REVERT: C 467 ASP cc_start: 0.5542 (t70) cc_final: 0.5195 (p0) REVERT: C 607 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8314 (mt0) REVERT: C 759 PHE cc_start: 0.6880 (m-80) cc_final: 0.6485 (t80) REVERT: C 856 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8806 (mmtp) REVERT: C 973 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.6975 (tp) REVERT: C 1113 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7878 (mm110) outliers start: 70 outliers final: 48 residues processed: 240 average time/residue: 0.4907 time to fit residues: 139.7751 Evaluate side-chains 233 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 177 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU 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 1058 HIS 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 A residue 1133 VAL 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 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 206 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 326 ILE 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 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 761 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 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: 9.9990 chunk 121 optimal weight: 0.0010 chunk 245 optimal weight: 0.6980 chunk 250 optimal weight: 0.7980 chunk 252 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 258 optimal weight: 0.0670 chunk 41 optimal weight: 3.9990 chunk 216 optimal weight: 0.0050 chunk 8 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 394 ASN A 751 ASN A 957 GLN B 87 ASN B 762 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.161135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114797 restraints weight = 23973.513| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.75 r_work: 0.3075 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 21443 Z= 0.101 Angle : 0.534 14.969 29221 Z= 0.272 Chirality : 0.046 0.593 3417 Planarity : 0.004 0.053 3697 Dihedral : 5.105 59.533 3294 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.04 % Favored : 96.73 % Rotamer: Outliers : 1.90 % Allowed : 19.15 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.16), residues: 2568 helix: 2.68 (0.20), residues: 625 sheet: 0.56 (0.20), residues: 594 loop : -1.03 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 646 TYR 0.017 0.001 TYR A1067 PHE 0.032 0.001 PHE B 592 TRP 0.015 0.001 TRP A 353 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00211 (21391) covalent geometry : angle 0.50328 (29095) SS BOND : bond 0.00271 ( 30) SS BOND : angle 1.01144 ( 60) hydrogen bonds : bond 0.03762 ( 937) hydrogen bonds : angle 5.18525 ( 2592) link_NAG-ASN : bond 0.00586 ( 22) link_NAG-ASN : angle 3.66665 ( 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 225 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5419 (OUTLIER) cc_final: 0.5105 (mt) REVERT: A 237 ARG cc_start: 0.7133 (mtp180) cc_final: 0.6906 (mtp85) REVERT: A 392 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7764 (m-80) REVERT: A 1117 THR cc_start: 0.7851 (m) cc_final: 0.7638 (p) REVERT: B 309 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8246 (mm-30) REVERT: C 118 LEU cc_start: 0.8157 (tp) cc_final: 0.7824 (tm) REVERT: C 241 LEU cc_start: 0.6710 (mt) cc_final: 0.6303 (pp) REVERT: C 338 PHE cc_start: 0.7418 (m-80) cc_final: 0.6990 (m-10) REVERT: C 357 ARG cc_start: 0.7299 (ttt-90) cc_final: 0.7033 (tmt170) REVERT: C 467 ASP cc_start: 0.5427 (t70) cc_final: 0.5198 (p0) REVERT: C 759 PHE cc_start: 0.6776 (m-80) cc_final: 0.6328 (t80) REVERT: C 856 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8829 (mmtp) REVERT: C 1117 THR cc_start: 0.8287 (t) cc_final: 0.8053 (p) outliers start: 43 outliers final: 25 residues processed: 215 average time/residue: 0.5203 time to fit residues: 131.7619 Evaluate side-chains 201 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 392 PHE Chi-restraints excluded: chain A residue 503 VAL 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 1058 HIS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN 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 791 THR Chi-restraints excluded: chain C residue 205 SER 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 615 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain H residue 99 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 134 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 0.0770 chunk 180 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 98 optimal weight: 0.0030 chunk 25 optimal weight: 0.5980 chunk 264 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.4348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3890 r_free = 0.3890 target = 0.160658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.113366 restraints weight = 24085.036| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.82 r_work: 0.3077 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 21443 Z= 0.109 Angle : 0.541 14.989 29221 Z= 0.277 Chirality : 0.047 0.592 3417 Planarity : 0.004 0.052 3697 Dihedral : 4.956 59.625 3286 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.50 % Favored : 96.26 % Rotamer: Outliers : 1.50 % Allowed : 19.33 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.16), residues: 2568 helix: 2.68 (0.20), residues: 625 sheet: 0.61 (0.20), residues: 597 loop : -0.98 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 646 TYR 0.017 0.001 TYR A1067 PHE 0.031 0.001 PHE B 592 TRP 0.019 0.001 TRP A 353 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00232 (21391) covalent geometry : angle 0.51145 (29095) SS BOND : bond 0.00276 ( 30) SS BOND : angle 1.18560 ( 60) hydrogen bonds : bond 0.03972 ( 937) hydrogen bonds : angle 5.19742 ( 2592) link_NAG-ASN : bond 0.00551 ( 22) link_NAG-ASN : angle 3.63661 ( 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 215 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5445 (OUTLIER) cc_final: 0.5155 (mt) REVERT: A 237 ARG cc_start: 0.7098 (mtp180) cc_final: 0.6873 (mtp85) REVERT: A 392 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.7697 (m-80) REVERT: A 1091 ARG cc_start: 0.7596 (mtm-85) cc_final: 0.6863 (mtt-85) REVERT: A 1117 THR cc_start: 0.7849 (m) cc_final: 0.7611 (p) REVERT: B 309 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8248 (mm-30) REVERT: C 241 LEU cc_start: 0.6779 (mt) cc_final: 0.6387 (pp) REVERT: C 338 PHE cc_start: 0.7431 (m-80) cc_final: 0.6997 (m-10) REVERT: C 357 ARG cc_start: 0.7278 (ttt-90) cc_final: 0.6919 (ttt90) REVERT: C 467 ASP cc_start: 0.5429 (t70) cc_final: 0.5213 (p0) REVERT: C 759 PHE cc_start: 0.6505 (m-80) cc_final: 0.6095 (t80) REVERT: C 856 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8811 (mmtp) REVERT: C 1117 THR cc_start: 0.8298 (t) cc_final: 0.8052 (p) outliers start: 34 outliers final: 26 residues processed: 209 average time/residue: 0.5089 time to fit residues: 125.6194 Evaluate side-chains 204 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 503 VAL 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 1058 HIS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN 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 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain C residue 205 SER 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 615 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 856 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 221 optimal weight: 0.5980 chunk 179 optimal weight: 7.9990 chunk 251 optimal weight: 0.5980 chunk 213 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 240 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.159797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.110426 restraints weight = 23969.523| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.80 r_work: 0.3031 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21443 Z= 0.127 Angle : 0.562 15.144 29221 Z= 0.289 Chirality : 0.047 0.602 3417 Planarity : 0.004 0.053 3697 Dihedral : 5.085 55.516 3286 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.54 % Favored : 96.22 % Rotamer: Outliers : 1.77 % Allowed : 19.06 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.16), residues: 2568 helix: 2.66 (0.20), residues: 619 sheet: 0.59 (0.20), residues: 600 loop : -0.99 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.020 0.001 TYR C 904 PHE 0.029 0.001 PHE B 592 TRP 0.019 0.001 TRP A 353 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00278 (21391) covalent geometry : angle 0.53115 (29095) SS BOND : bond 0.00315 ( 30) SS BOND : angle 1.26721 ( 60) hydrogen bonds : bond 0.04326 ( 937) hydrogen bonds : angle 5.34658 ( 2592) link_NAG-ASN : bond 0.00563 ( 22) link_NAG-ASN : angle 3.73103 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9771.20 seconds wall clock time: 167 minutes 14.42 seconds (10034.42 seconds total)