Starting phenix.real_space_refine on Wed Jun 18 10:19:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3m_34469/06_2025/8h3m_34469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3m_34469/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h3m_34469/06_2025/8h3m_34469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3m_34469/06_2025/8h3m_34469.map" model { file = "/net/cci-nas-00/data/ceres_data/8h3m_34469/06_2025/8h3m_34469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3m_34469/06_2025/8h3m_34469.cif" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP: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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, '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: 13.87, per 1000 atoms: 0.66 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: 5.03 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 3.36 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: 9.11 Time building geometry restraints manager: 5.93 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: 7.750 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: 0.940 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 50.740 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.480 ------------------------------------------------------------------------------- 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 : 5.84 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (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 TRP 0.013 0.001 TRP A 353 HIS 0.004 0.001 HIS A1048 PHE 0.036 0.001 PHE B 592 TYR 0.016 0.001 TYR C1067 ARG 0.006 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00764 ( 22) link_NAG-ASN : angle 4.36494 ( 66) hydrogen bonds : bond 0.13127 ( 937) hydrogen bonds : angle 7.06744 ( 2592) SS BOND : bond 0.00363 ( 30) SS BOND : angle 1.42671 ( 60) covalent geometry : bond 0.00358 (21391) covalent geometry : angle 0.64598 (29095) *********************** 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 : 2.356 Fit side-chains revert: symmetry clash 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: 0.7843 (mm-30) outliers start: 46 outliers final: 38 residues processed: 234 average time/residue: 1.0626 time to fit residues: 293.6647 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 : 2.247 ------------------------------------------------------------------------------- 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 223 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 240 optimal weight: 0.0870 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.159490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112256 restraints weight = 24007.238| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.67 r_work: 0.3050 rms_B_bonded: 2.14 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: 0.8516 moved from start: 0.0613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21443 Z= 0.134 Angle : 0.597 17.436 29221 Z= 0.305 Chirality : 0.048 0.670 3417 Planarity : 0.004 0.061 3697 Dihedral : 6.969 60.611 3326 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.78 % Favored : 95.95 % Rotamer: Outliers : 3.05 % Allowed : 14.92 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2568 helix: 2.47 (0.20), residues: 610 sheet: 0.52 (0.20), residues: 582 loop : -1.10 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.007 0.001 HIS A1083 PHE 0.029 0.001 PHE B 592 TYR 0.019 0.001 TYR B1067 ARG 0.004 0.000 ARG C 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 22) link_NAG-ASN : angle 4.09712 ( 66) hydrogen bonds : bond 0.04583 ( 937) hydrogen bonds : angle 5.71689 ( 2592) SS BOND : bond 0.00327 ( 30) SS BOND : angle 1.30554 ( 60) covalent geometry : bond 0.00290 (21391) covalent geometry : angle 0.56234 (29095) *********************** 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 259 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 190 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1045 LYS cc_start: 0.7712 (tppp) cc_final: 0.7338 (tptt) REVERT: A 1117 THR cc_start: 0.7868 (m) cc_final: 0.7613 (p) REVERT: B 309 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8196 (mm-30) REVERT: B 965 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: C 357 ARG cc_start: 0.6058 (tpt170) cc_final: 0.5724 (tpt170) REVERT: C 467 ASP cc_start: 0.5594 (t70) cc_final: 0.5354 (m-30) REVERT: C 607 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: H 96 LYS cc_start: 0.6489 (OUTLIER) cc_final: 0.6056 (mptt) outliers start: 69 outliers final: 34 residues processed: 240 average time/residue: 1.0130 time to fit residues: 286.7758 Evaluate side-chains 218 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 616 ASN 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 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 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 900 MET 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 61 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 762 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3857 r_free = 0.3857 target = 0.157791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.109214 restraints weight = 23759.448| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.77 r_work: 0.3002 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 21443 Z= 0.199 Angle : 0.655 18.245 29221 Z= 0.336 Chirality : 0.051 0.798 3417 Planarity : 0.005 0.050 3697 Dihedral : 6.372 59.164 3300 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.21 % Favored : 95.52 % Rotamer: Outliers : 3.18 % Allowed : 15.53 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2568 helix: 2.39 (0.21), residues: 605 sheet: 0.43 (0.20), residues: 578 loop : -1.19 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 633 HIS 0.005 0.001 HIS A1083 PHE 0.026 0.002 PHE B 592 TYR 0.018 0.002 TYR B1067 ARG 0.004 0.001 ARG C 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 22) link_NAG-ASN : angle 4.40412 ( 66) hydrogen bonds : bond 0.05351 ( 937) hydrogen bonds : angle 5.87186 ( 2592) SS BOND : bond 0.00428 ( 30) SS BOND : angle 1.54096 ( 60) covalent geometry : bond 0.00453 (21391) covalent geometry : angle 0.61804 (29095) *********************** 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 257 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 185 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 973 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8408 (pp) REVERT: A 1107 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7999 (mtt180) REVERT: A 1117 THR cc_start: 0.7941 (m) cc_final: 0.7713 (p) REVERT: B 309 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8243 (mm-30) REVERT: C 338 PHE cc_start: 0.7379 (m-80) cc_final: 0.7034 (m-10) REVERT: C 467 ASP cc_start: 0.5570 (t70) cc_final: 0.5030 (p0) REVERT: C 607 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8341 (mt0) REVERT: C 675 GLN cc_start: 0.6382 (OUTLIER) cc_final: 0.5498 (pt0) REVERT: C 856 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8203 (mtpp) REVERT: C 973 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6856 (tp) outliers start: 72 outliers final: 44 residues processed: 235 average time/residue: 1.0061 time to fit residues: 279.7032 Evaluate side-chains 227 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 2.151 ------------------------------------------------------------------------------- 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 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 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 1058 HIS Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain 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 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 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 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 675 GLN 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 7 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 147 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 236 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 957 GLN B 957 GLN C 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110343 restraints weight = 24175.124| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.79 r_work: 0.3026 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 21443 Z= 0.136 Angle : 0.582 16.934 29221 Z= 0.298 Chirality : 0.048 0.736 3417 Planarity : 0.004 0.044 3697 Dihedral : 5.833 59.234 3296 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.47 % Favored : 96.26 % Rotamer: Outliers : 3.13 % Allowed : 16.06 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.16), residues: 2568 helix: 2.52 (0.20), residues: 617 sheet: 0.48 (0.21), residues: 571 loop : -1.10 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 633 HIS 0.003 0.001 HIS A1048 PHE 0.029 0.001 PHE B 592 TYR 0.017 0.001 TYR B1067 ARG 0.004 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00492 ( 22) link_NAG-ASN : angle 4.03574 ( 66) hydrogen bonds : bond 0.04499 ( 937) hydrogen bonds : angle 5.56462 ( 2592) SS BOND : bond 0.00323 ( 30) SS BOND : angle 1.32503 ( 60) covalent geometry : bond 0.00298 (21391) covalent geometry : angle 0.54704 (29095) *********************** 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 259 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 188 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7284 (mtp180) cc_final: 0.7036 (mtp85) REVERT: A 973 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8381 (pp) REVERT: A 1117 THR cc_start: 0.7952 (m) cc_final: 0.7730 (p) REVERT: B 309 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8263 (mm-30) REVERT: B 965 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: C 338 PHE cc_start: 0.7411 (m-80) cc_final: 0.7017 (m-10) REVERT: C 467 ASP cc_start: 0.5568 (t70) cc_final: 0.5089 (p0) REVERT: C 607 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8333 (mt0) REVERT: C 759 PHE cc_start: 0.6865 (m-80) cc_final: 0.6445 (t80) REVERT: C 973 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6729 (tp) REVERT: C 1113 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7860 (mm110) outliers start: 71 outliers final: 42 residues processed: 238 average time/residue: 1.0073 time to fit residues: 283.3371 Evaluate side-chains 226 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain 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 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 957 GLN Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 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 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 170 optimal weight: 10.0000 chunk 190 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 108 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 81 ASN B 762 GLN C 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.157970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.108663 restraints weight = 23987.165| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.85 r_work: 0.2998 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 21443 Z= 0.185 Angle : 0.631 16.972 29221 Z= 0.324 Chirality : 0.051 0.687 3417 Planarity : 0.005 0.046 3697 Dihedral : 6.019 58.572 3295 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.56 % Favored : 95.17 % Rotamer: Outliers : 3.31 % Allowed : 16.20 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2568 helix: 2.44 (0.20), residues: 606 sheet: 0.42 (0.21), residues: 578 loop : -1.10 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 633 HIS 0.003 0.001 HIS A1048 PHE 0.029 0.002 PHE B 592 TYR 0.018 0.002 TYR B1067 ARG 0.005 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00558 ( 22) link_NAG-ASN : angle 4.20552 ( 66) hydrogen bonds : bond 0.05076 ( 937) hydrogen bonds : angle 5.72511 ( 2592) SS BOND : bond 0.00431 ( 30) SS BOND : angle 1.47927 ( 60) covalent geometry : bond 0.00418 (21391) covalent geometry : angle 0.59648 (29095) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 182 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 973 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8423 (pp) REVERT: A 1117 THR cc_start: 0.7985 (m) cc_final: 0.7781 (p) REVERT: B 740 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8557 (tpt) REVERT: C 338 PHE cc_start: 0.7394 (m-80) cc_final: 0.7010 (m-10) REVERT: C 467 ASP cc_start: 0.5569 (t70) cc_final: 0.5092 (p0) REVERT: C 607 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8351 (mt0) REVERT: C 759 PHE cc_start: 0.6966 (m-80) cc_final: 0.6633 (t80) REVERT: C 856 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8840 (mmtp) REVERT: C 973 ILE cc_start: 0.7173 (OUTLIER) cc_final: 0.6814 (tp) REVERT: C 1113 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7693 (mm110) outliers start: 75 outliers final: 45 residues processed: 238 average time/residue: 0.9571 time to fit residues: 271.3335 Evaluate side-chains 229 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER 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 916 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain 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 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 38 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 250 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 B 762 GLN C 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.157535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109226 restraints weight = 23937.860| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.71 r_work: 0.3020 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 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 : 0.004 0.085 21443 Z= 0.196 Angle : 0.646 17.350 29221 Z= 0.331 Chirality : 0.051 0.770 3417 Planarity : 0.005 0.051 3697 Dihedral : 6.105 58.420 3295 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.52 % Favored : 95.25 % Rotamer: Outliers : 3.66 % Allowed : 16.28 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2568 helix: 2.36 (0.20), residues: 609 sheet: 0.37 (0.20), residues: 590 loop : -1.12 (0.16), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 633 HIS 0.004 0.001 HIS A1048 PHE 0.029 0.002 PHE B 592 TYR 0.018 0.002 TYR A1067 ARG 0.005 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 22) link_NAG-ASN : angle 4.26758 ( 66) hydrogen bonds : bond 0.05190 ( 937) hydrogen bonds : angle 5.77457 ( 2592) SS BOND : bond 0.00446 ( 30) SS BOND : angle 1.47983 ( 60) covalent geometry : bond 0.00448 (21391) covalent geometry : angle 0.61148 (29095) *********************** 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 273 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 190 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 ARG cc_start: 0.5530 (OUTLIER) cc_final: 0.4935 (ptm-80) REVERT: A 973 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8402 (pp) REVERT: A 1107 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8029 (mtt180) REVERT: B 740 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8547 (tpt) REVERT: C 338 PHE cc_start: 0.7404 (m-80) cc_final: 0.7029 (m-10) REVERT: C 357 ARG cc_start: 0.7539 (ttt-90) cc_final: 0.7277 (ttt180) REVERT: C 467 ASP cc_start: 0.5572 (t70) cc_final: 0.5110 (p0) REVERT: C 607 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8318 (mt0) REVERT: C 675 GLN cc_start: 0.6377 (OUTLIER) cc_final: 0.5394 (pt0) REVERT: C 759 PHE cc_start: 0.7046 (m-80) cc_final: 0.6720 (t80) REVERT: C 856 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8823 (mmtp) REVERT: C 973 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6808 (tp) REVERT: C 1113 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7639 (mm110) outliers start: 83 outliers final: 51 residues processed: 253 average time/residue: 0.9949 time to fit residues: 298.3996 Evaluate side-chains 240 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 180 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER 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 403 ARG Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 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 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 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 675 GLN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 40 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** B 87 ASN B 762 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.158758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.110293 restraints weight = 23914.665| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.78 r_work: 0.3017 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21443 Z= 0.141 Angle : 0.594 16.377 29221 Z= 0.304 Chirality : 0.048 0.671 3417 Planarity : 0.004 0.051 3697 Dihedral : 5.731 57.910 3294 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.86 % Favored : 95.91 % Rotamer: Outliers : 3.27 % Allowed : 17.21 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2568 helix: 2.48 (0.20), residues: 619 sheet: 0.44 (0.20), residues: 588 loop : -1.10 (0.16), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.003 0.001 HIS A1048 PHE 0.032 0.001 PHE B 592 TYR 0.017 0.001 TYR B1067 ARG 0.005 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 22) link_NAG-ASN : angle 4.07306 ( 66) hydrogen bonds : bond 0.04590 ( 937) hydrogen bonds : angle 5.57798 ( 2592) SS BOND : bond 0.00409 ( 30) SS BOND : angle 1.27004 ( 60) covalent geometry : bond 0.00311 (21391) covalent geometry : angle 0.55961 (29095) *********************** 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 259 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 185 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7256 (mtp180) cc_final: 0.6969 (mtp85) REVERT: A 392 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7736 (m-80) REVERT: A 1107 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.8030 (mtt180) REVERT: B 309 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8281 (mm-30) REVERT: B 740 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8464 (tpt) REVERT: C 101 ILE cc_start: 0.6122 (OUTLIER) cc_final: 0.5852 (tp) REVERT: C 206 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7980 (tttp) REVERT: C 338 PHE cc_start: 0.7415 (m-80) cc_final: 0.6985 (m-10) REVERT: C 357 ARG cc_start: 0.7466 (ttt-90) cc_final: 0.7104 (tmt170) REVERT: C 467 ASP cc_start: 0.5494 (t70) cc_final: 0.5173 (p0) REVERT: C 607 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8338 (mt0) REVERT: C 759 PHE cc_start: 0.6935 (m-80) cc_final: 0.6566 (t80) REVERT: C 856 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8841 (mmtp) REVERT: C 1113 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7734 (mm110) outliers start: 74 outliers final: 47 residues processed: 242 average time/residue: 1.0221 time to fit residues: 296.0636 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 : 2.163 ------------------------------------------------------------------------------- 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 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 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 1120 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 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 153 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 240 optimal weight: 0.3980 chunk 220 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 247 optimal weight: 0.8980 chunk 187 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 394 ASN A 751 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.159190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.110297 restraints weight = 24128.751| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.77 r_work: 0.3036 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21443 Z= 0.133 Angle : 0.578 16.734 29221 Z= 0.295 Chirality : 0.048 0.739 3417 Planarity : 0.004 0.052 3697 Dihedral : 5.561 59.876 3294 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.01 % Favored : 95.76 % Rotamer: Outliers : 2.87 % Allowed : 17.61 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2568 helix: 2.55 (0.20), residues: 620 sheet: 0.50 (0.20), residues: 583 loop : -1.08 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.003 0.001 HIS A1048 PHE 0.030 0.001 PHE B 592 TYR 0.017 0.001 TYR B1067 ARG 0.006 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 22) link_NAG-ASN : angle 3.98828 ( 66) hydrogen bonds : bond 0.04430 ( 937) hydrogen bonds : angle 5.48004 ( 2592) SS BOND : bond 0.00377 ( 30) SS BOND : angle 1.16435 ( 60) covalent geometry : bond 0.00291 (21391) covalent geometry : angle 0.54443 (29095) *********************** 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 253 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7235 (mtp180) cc_final: 0.6959 (mtp85) REVERT: A 392 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: A 403 ARG cc_start: 0.5522 (OUTLIER) cc_final: 0.4822 (ptm-80) REVERT: A 1107 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8021 (mtt180) REVERT: B 309 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8276 (mm-30) REVERT: B 740 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8450 (tpt) REVERT: C 101 ILE cc_start: 0.6111 (OUTLIER) cc_final: 0.5841 (tp) REVERT: C 206 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.7979 (tttp) REVERT: C 338 PHE cc_start: 0.7354 (m-80) cc_final: 0.6910 (m-10) REVERT: C 357 ARG cc_start: 0.7433 (ttt-90) cc_final: 0.7095 (tmt170) REVERT: C 467 ASP cc_start: 0.5515 (t70) cc_final: 0.5211 (p0) REVERT: C 607 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8312 (mt0) REVERT: C 759 PHE cc_start: 0.6913 (m-80) cc_final: 0.6515 (t80) REVERT: C 856 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8819 (mmtp) REVERT: C 1113 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7885 (mm110) outliers start: 65 outliers final: 44 residues processed: 238 average time/residue: 1.1527 time to fit residues: 324.3431 Evaluate side-chains 235 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 182 time to evaluate : 2.767 ------------------------------------------------------------------------------- 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 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 403 ARG Chi-restraints excluded: chain A residue 430 THR 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 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 638 THR 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 957 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 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 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain H residue 99 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 259 optimal weight: 0.5980 chunk 117 optimal weight: 0.0980 chunk 169 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 236 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.159795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.110714 restraints weight = 24062.735| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.70 r_work: 0.3063 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21443 Z= 0.120 Angle : 0.558 15.785 29221 Z= 0.286 Chirality : 0.047 0.649 3417 Planarity : 0.004 0.052 3697 Dihedral : 5.208 55.325 3289 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.58 % Favored : 96.18 % Rotamer: Outliers : 2.60 % Allowed : 18.14 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2568 helix: 2.61 (0.20), residues: 625 sheet: 0.53 (0.20), residues: 598 loop : -1.08 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 353 HIS 0.003 0.001 HIS A1048 PHE 0.030 0.001 PHE B 592 TYR 0.017 0.001 TYR B1067 ARG 0.006 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 22) link_NAG-ASN : angle 3.82867 ( 66) hydrogen bonds : bond 0.04203 ( 937) hydrogen bonds : angle 5.37153 ( 2592) SS BOND : bond 0.00351 ( 30) SS BOND : angle 1.09402 ( 60) covalent geometry : bond 0.00260 (21391) covalent geometry : angle 0.52668 (29095) *********************** 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 248 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7153 (mtp180) cc_final: 0.6907 (mtp85) REVERT: A 281 GLU cc_start: 0.6989 (mp0) cc_final: 0.6764 (mm-30) REVERT: A 340 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6473 (mp0) REVERT: A 392 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7778 (m-80) REVERT: A 403 ARG cc_start: 0.5486 (OUTLIER) cc_final: 0.5274 (ttm170) REVERT: A 1107 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7931 (mtt180) REVERT: B 309 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8225 (mm-30) REVERT: B 740 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8361 (tpt) REVERT: C 101 ILE cc_start: 0.6129 (OUTLIER) cc_final: 0.5856 (tp) REVERT: C 206 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7986 (tttp) REVERT: C 241 LEU cc_start: 0.6626 (mt) cc_final: 0.6184 (pp) REVERT: C 338 PHE cc_start: 0.7427 (m-80) cc_final: 0.6964 (m-10) REVERT: C 357 ARG cc_start: 0.7377 (ttt-90) cc_final: 0.7034 (tmt170) REVERT: C 467 ASP cc_start: 0.5465 (t70) cc_final: 0.5212 (p0) REVERT: C 759 PHE cc_start: 0.6868 (m-80) cc_final: 0.6470 (t80) REVERT: C 856 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8812 (mmtp) REVERT: C 1117 THR cc_start: 0.8336 (t) cc_final: 0.8045 (p) REVERT: H 34 MET cc_start: 0.3976 (mmm) cc_final: 0.3663 (mmm) outliers start: 59 outliers final: 43 residues processed: 234 average time/residue: 1.0017 time to fit residues: 278.5957 Evaluate side-chains 233 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER 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 403 ARG Chi-restraints excluded: chain A residue 430 THR 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 1058 HIS Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 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 638 THR 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 957 GLN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 6 optimal weight: 7.9990 chunk 104 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN 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** C1113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.157551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.108014 restraints weight = 23939.042| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.72 r_work: 0.3013 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 21443 Z= 0.214 Angle : 0.661 17.042 29221 Z= 0.339 Chirality : 0.051 0.723 3417 Planarity : 0.005 0.052 3697 Dihedral : 5.767 55.124 3287 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.79 % Favored : 94.98 % Rotamer: Outliers : 2.56 % Allowed : 18.09 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 2568 helix: 2.40 (0.20), residues: 608 sheet: 0.35 (0.20), residues: 602 loop : -1.10 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.004 0.001 HIS A 207 PHE 0.027 0.002 PHE B 86 TYR 0.022 0.002 TYR C 904 ARG 0.003 0.001 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 22) link_NAG-ASN : angle 4.28410 ( 66) hydrogen bonds : bond 0.05292 ( 937) hydrogen bonds : angle 5.76787 ( 2592) SS BOND : bond 0.00466 ( 30) SS BOND : angle 1.76134 ( 60) covalent geometry : bond 0.00492 (21391) covalent geometry : angle 0.62462 (29095) ********************** 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 242 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 184 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7243 (mtp180) cc_final: 0.6951 (mtp85) REVERT: A 392 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: A 403 ARG cc_start: 0.5517 (OUTLIER) cc_final: 0.4688 (ptm-80) REVERT: A 1107 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8037 (mtt180) REVERT: B 740 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8541 (tpt) REVERT: C 101 ILE cc_start: 0.6180 (OUTLIER) cc_final: 0.5941 (tp) REVERT: C 357 ARG cc_start: 0.7476 (ttt-90) cc_final: 0.7127 (tmt170) REVERT: C 467 ASP cc_start: 0.5583 (t70) cc_final: 0.5225 (p0) REVERT: C 759 PHE cc_start: 0.6746 (m-80) cc_final: 0.6468 (t80) REVERT: C 856 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8802 (mmtp) REVERT: H 34 MET cc_start: 0.3809 (mmm) cc_final: 0.3501 (mmm) outliers start: 58 outliers final: 45 residues processed: 229 average time/residue: 1.0744 time to fit residues: 293.4227 Evaluate side-chains 228 residues out of total 2337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER 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 403 ARG 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 916 LEU 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 47 VAL Chi-restraints excluded: chain B residue 284 THR 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 638 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 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 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 166 optimal weight: 3.9990 chunk 204 optimal weight: 9.9990 chunk 231 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 127 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 251 optimal weight: 0.5980 chunk 221 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.109734 restraints weight = 23969.673| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.61 r_work: 0.3070 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21443 Z= 0.133 Angle : 0.582 15.938 29221 Z= 0.298 Chirality : 0.048 0.658 3417 Planarity : 0.004 0.053 3697 Dihedral : 5.328 50.479 3287 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.70 % Favored : 96.07 % Rotamer: Outliers : 2.25 % Allowed : 18.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 2568 helix: 2.55 (0.20), residues: 618 sheet: 0.44 (0.20), residues: 586 loop : -1.09 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 353 HIS 0.003 0.001 HIS A1048 PHE 0.028 0.001 PHE B 592 TYR 0.017 0.001 TYR B1067 ARG 0.006 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 22) link_NAG-ASN : angle 4.03619 ( 66) hydrogen bonds : bond 0.04422 ( 937) hydrogen bonds : angle 5.50060 ( 2592) SS BOND : bond 0.00327 ( 30) SS BOND : angle 1.28765 ( 60) covalent geometry : bond 0.00293 (21391) covalent geometry : angle 0.54716 (29095) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18436.97 seconds wall clock time: 316 minutes 19.89 seconds (18979.89 seconds total)