Starting phenix.real_space_refine on Tue May 27 19:18:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r1d_18808/05_2025/8r1d_18808.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r1d_18808/05_2025/8r1d_18808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r1d_18808/05_2025/8r1d_18808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r1d_18808/05_2025/8r1d_18808.map" model { file = "/net/cci-nas-00/data/ceres_data/8r1d_18808/05_2025/8r1d_18808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r1d_18808/05_2025/8r1d_18808.cif" } resolution = 2.37 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= 0.008 sd= 0.083 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 138 5.16 5 C 19377 2.51 5 N 5043 2.21 5 O 5935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.48s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30493 Number of models: 1 Model: "" Number of chains: 18 Chain: "F" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 905 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "D" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 905 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "H" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 905 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "A" Number of atoms: 8317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8317 Classifications: {'peptide': 1065} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1014} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8317 Classifications: {'peptide': 1065} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1014} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8317 Classifications: {'peptide': 1065} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1014} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "G" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 18.30, per 1000 atoms: 0.60 Number of scatterers: 30493 At special positions: 0 Unit cell: (170.16, 162.857, 172.351, 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 138 16.00 O 5935 8.00 N 5043 7.00 C 19377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 106 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 106 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.04 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 87 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 58 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 613 " " NAG A1304 " - " ASN A 654 " " NAG A1305 " - " ASN A1071 " " NAG A1306 " - " ASN A 714 " " NAG A1307 " - " ASN A 798 " " NAG A1308 " - " ASN A1131 " " NAG A1309 " - " ASN A 231 " " NAG A1310 " - " ASN A 706 " " NAG B1301 " - " ASN B 58 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 613 " " NAG B1304 " - " ASN B 654 " " NAG B1305 " - " ASN B1071 " " NAG B1306 " - " ASN B 714 " " NAG B1307 " - " ASN B 798 " " NAG B1308 " - " ASN B1131 " " NAG B1309 " - " ASN B 231 " " NAG B1310 " - " ASN B 706 " " NAG C1301 " - " ASN C 58 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 613 " " NAG C1304 " - " ASN C 654 " " NAG C1305 " - " ASN C1071 " " NAG C1306 " - " ASN C 714 " " NAG C1307 " - " ASN C 798 " " NAG C1308 " - " ASN C1131 " " NAG C1309 " - " ASN C 231 " " NAG C1310 " - " ASN C 706 " Time building additional restraints: 7.44 Conformation dependent library (CDL) restraints added in 3.9 seconds 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7188 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 68 sheets defined 23.5% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.23 Creating SS restraints... Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.641A pdb=" N PHE A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.529A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.665A pdb=" N SER A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.607A pdb=" N SER A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 613 through 617 Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.637A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 removed outlier: 3.510A pdb=" N VAL A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 853 removed outlier: 3.889A pdb=" N ALA A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.880A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 909 through 916 removed outlier: 3.987A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 3.823A pdb=" N VAL A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.222A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.709A pdb=" N PHE B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 369' Processing helix chain 'B' and resid 380 through 386 removed outlier: 3.552A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.502A pdb=" N SER B 405 " --> pdb=" O ASN B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.642A pdb=" N SER B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 613 through 617 Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 752 removed outlier: 4.001A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.673A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 845 through 853 removed outlier: 3.921A pdb=" N ALA B 849 " --> pdb=" O ASP B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.805A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 909 through 916 removed outlier: 3.918A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 3.782A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 4.281A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 361 through 363 No H-bonds generated for 'chain 'C' and resid 361 through 363' Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.664A pdb=" N PHE C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.557A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.631A pdb=" N SER C 405 " --> pdb=" O ASN C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 removed outlier: 3.604A pdb=" N SER C 440 " --> pdb=" O ASN C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 613 through 617 Processing helix chain 'C' and resid 734 through 741 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.648A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 removed outlier: 3.508A pdb=" N VAL C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 853 removed outlier: 3.915A pdb=" N ALA C 849 " --> pdb=" O ASP C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.915A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 909 through 916 removed outlier: 3.947A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 3.775A pdb=" N VAL C 988 " --> pdb=" O VAL C 984 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 4.276A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 30 Processing helix chain 'E' and resid 78 through 82 Processing helix chain 'G' and resid 26 through 30 Processing helix chain 'G' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain 'F' and resid 3 through 7 removed outlier: 5.902A pdb=" N GLY F 16 " --> pdb=" O SER F 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.318A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.994A pdb=" N TYR F 110 " --> pdb=" O THR F 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.287A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.975A pdb=" N TYR D 110 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.236A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.034A pdb=" N TYR H 110 " --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.469A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB4, first strand: chain 'A' and resid 20 through 27 removed outlier: 7.833A pdb=" N ASN A 58 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR A 266 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE A 198 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP A 225 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 200 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 44 through 52 removed outlier: 3.845A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AB7, first strand: chain 'A' and resid 81 through 82 removed outlier: 4.096A pdb=" N GLY A 100 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA A 240 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 98 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 129 through 132 removed outlier: 6.313A pdb=" N GLU A 129 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA A 160 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLN A 131 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 626 through 627 removed outlier: 4.471A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.259A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AC3, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.743A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AC5, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AC6, first strand: chain 'A' and resid 651 through 657 removed outlier: 6.004A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL A 653 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 699 through 701 Processing sheet with id=AC8, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.754A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 715 through 725 removed outlier: 5.854A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.300A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 785 through 787 removed outlier: 6.115A pdb=" N ILE A 785 " --> pdb=" O ASN B 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AD4, first strand: chain 'B' and resid 20 through 27 removed outlier: 7.956A pdb=" N ASN B 58 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR B 266 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N PHE B 198 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP B 225 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B 200 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 44 through 52 removed outlier: 3.779A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 81 through 82 removed outlier: 12.689A pdb=" N PHE B 235 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ASN B 134 " --> pdb=" O PHE B 235 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N THR B 237 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU B 239 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU B 129 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA B 160 " --> pdb=" O GLU B 129 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN B 131 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B 156 " --> pdb=" O CYS B 133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 81 through 82 removed outlier: 4.128A pdb=" N GLY B 100 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA B 240 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE B 98 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 626 through 627 removed outlier: 4.429A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.247A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AE2, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.641A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AE4, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AE5, first strand: chain 'B' and resid 651 through 657 removed outlier: 6.035A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL B 653 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.798A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 715 through 725 removed outlier: 5.906A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.352A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 785 through 787 removed outlier: 6.188A pdb=" N ILE B 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'B' and resid 1117 through 1119 Processing sheet with id=AF2, first strand: chain 'C' and resid 20 through 27 removed outlier: 7.903A pdb=" N ASN C 58 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TYR C 266 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE C 198 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP C 225 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE C 200 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 44 through 52 removed outlier: 3.849A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AF5, first strand: chain 'C' and resid 81 through 82 removed outlier: 4.281A pdb=" N GLY C 100 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA C 240 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE C 98 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 129 through 132 removed outlier: 3.735A pdb=" N ASN C 161 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER C 159 " --> pdb=" O GLN C 131 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 626 through 627 removed outlier: 4.542A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 321 through 325 removed outlier: 4.285A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AG1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.671A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AG3, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AG4, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.054A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 708 through 712 removed outlier: 3.763A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 715 through 725 removed outlier: 5.860A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.404A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AG9, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.491A pdb=" N TRP E 34 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 9 through 12 Processing sheet with id=AH2, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AH3, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.650A pdb=" N ALA G 83 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP G 34 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.650A pdb=" N ALA G 83 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 18 through 23 1362 hydrogen bonds defined for protein. 3582 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: 16.31 Time building geometry restraints manager: 8.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.69 - 0.91: 1 0.91 - 1.14: 1 1.14 - 1.37: 9872 1.37 - 1.59: 21089 1.59 - 1.82: 177 Bond restraints: 31140 Sorted by residual: bond pdb=" CG PRO L 8 " pdb=" CD PRO L 8 " ideal model delta sigma weight residual 1.503 0.686 0.817 3.40e-02 8.65e+02 5.77e+02 bond pdb=" CG PRO E 58 " pdb=" CD PRO E 58 " ideal model delta sigma weight residual 1.503 1.146 0.357 3.40e-02 8.65e+02 1.10e+02 bond pdb=" CG PRO H 41 " pdb=" CD PRO H 41 " ideal model delta sigma weight residual 1.503 1.156 0.347 3.40e-02 8.65e+02 1.04e+02 bond pdb=" CB PRO D 41 " pdb=" CG PRO D 41 " ideal model delta sigma weight residual 1.492 0.989 0.503 5.00e-02 4.00e+02 1.01e+02 bond pdb=" CG PRO G 58 " pdb=" CD PRO G 58 " ideal model delta sigma weight residual 1.503 1.183 0.320 3.40e-02 8.65e+02 8.86e+01 ... (remaining 31135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.76: 42358 14.76 - 29.52: 8 29.52 - 44.28: 2 44.28 - 59.04: 0 59.04 - 73.80: 1 Bond angle restraints: 42369 Sorted by residual: angle pdb=" N PRO L 8 " pdb=" CD PRO L 8 " pdb=" CG PRO L 8 " ideal model delta sigma weight residual 103.20 66.97 36.23 1.50e+00 4.44e-01 5.83e+02 angle pdb=" CB PRO D 41 " pdb=" CG PRO D 41 " pdb=" CD PRO D 41 " ideal model delta sigma weight residual 106.10 179.90 -73.80 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO D 41 " pdb=" CD PRO D 41 " pdb=" CG PRO D 41 " ideal model delta sigma weight residual 103.20 75.95 27.25 1.50e+00 4.44e-01 3.30e+02 angle pdb=" CA PRO D 41 " pdb=" CB PRO D 41 " pdb=" CG PRO D 41 " ideal model delta sigma weight residual 104.50 73.55 30.95 1.90e+00 2.77e-01 2.65e+02 angle pdb=" N PRO G 58 " pdb=" CD PRO G 58 " pdb=" CG PRO G 58 " ideal model delta sigma weight residual 103.20 79.50 23.70 1.50e+00 4.44e-01 2.50e+02 ... (remaining 42364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17072 17.92 - 35.85: 1297 35.85 - 53.77: 366 53.77 - 71.70: 85 71.70 - 89.62: 50 Dihedral angle restraints: 18870 sinusoidal: 7650 harmonic: 11220 Sorted by residual: dihedral pdb=" N PRO D 41 " pdb=" CG PRO D 41 " pdb=" CD PRO D 41 " pdb=" CB PRO D 41 " ideal model delta sinusoidal sigma weight residual -30.00 -118.45 88.45 1 1.50e+01 4.44e-03 4.15e+01 dihedral pdb=" CA THR B 596 " pdb=" C THR B 596 " pdb=" N PRO B 597 " pdb=" CA PRO B 597 " ideal model delta harmonic sigma weight residual 180.00 148.86 31.14 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA THR C 596 " pdb=" C THR C 596 " pdb=" N PRO C 597 " pdb=" CA PRO C 597 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 18867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4111 0.063 - 0.126: 727 0.126 - 0.188: 41 0.188 - 0.251: 3 0.251 - 0.314: 2 Chirality restraints: 4884 Sorted by residual: chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A 798 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 654 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 654 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 4881 not shown) Planarity restraints: 5460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 13 " 0.105 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO E 14 " -0.260 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 13 " -0.084 5.00e-02 4.00e+02 1.23e-01 2.40e+01 pdb=" N PRO L 14 " 0.212 5.00e-02 4.00e+02 pdb=" CA PRO L 14 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO L 14 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 7 " 0.083 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO G 8 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO G 8 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO G 8 " 0.066 5.00e-02 4.00e+02 ... (remaining 5457 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 482 2.67 - 3.23: 27656 3.23 - 3.78: 47892 3.78 - 4.34: 69841 4.34 - 4.90: 111080 Nonbonded interactions: 256951 Sorted by model distance: nonbonded pdb=" OG1 THR A 596 " pdb=" O PRO A 597 " model vdw 2.112 3.040 nonbonded pdb=" OG1 THR B 596 " pdb=" O PRO B 597 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR C 596 " pdb=" O PRO C 597 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR A 106 " pdb=" OG1 THR A 111 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR C 753 " pdb=" OD1 ASP C 991 " model vdw 2.222 3.040 ... (remaining 256946 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.440 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 73.210 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.160 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:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.008 0.817 31221 Z= 0.264 Angle : 0.875 73.796 42561 Z= 0.461 Chirality : 0.047 0.314 4884 Planarity : 0.006 0.150 5430 Dihedral : 14.944 89.619 11529 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.11 % Allowed : 13.54 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -0.07 (0.13), residues: 3822 helix: 1.57 (0.19), residues: 720 sheet: 0.17 (0.15), residues: 999 loop : -0.71 (0.12), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 630 HIS 0.004 0.001 HIS A1080 PHE 0.015 0.001 PHE C 315 TYR 0.018 0.002 TYR C1064 ARG 0.007 0.001 ARG B 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 30) link_NAG-ASN : angle 4.92442 ( 90) hydrogen bonds : bond 0.16042 ( 1325) hydrogen bonds : angle 7.59389 ( 3582) SS BOND : bond 0.00220 ( 51) SS BOND : angle 0.78812 ( 102) covalent geometry : bond 0.00801 (31140) covalent geometry : angle 0.84624 (42369) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 331 time to evaluate : 3.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.6187 (t0) cc_final: 0.5625 (t0) REVERT: B 495 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7576 (mtt90) REVERT: C 490 ARG cc_start: 0.7850 (tpp-160) cc_final: 0.7525 (tpp80) REVERT: G 11 SER cc_start: 0.6222 (OUTLIER) cc_final: 0.5929 (t) REVERT: G 58 PRO cc_start: 0.7150 (OUTLIER) cc_final: 0.6853 (Cg_exo) outliers start: 37 outliers final: 28 residues processed: 360 average time/residue: 1.3276 time to fit residues: 568.4418 Evaluate side-chains 353 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 323 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 58 PRO Chi-restraints excluded: chain G residue 71 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 161 optimal weight: 30.0000 chunk 99 optimal weight: 9.9990 chunk 196 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 300 optimal weight: 0.0980 chunk 116 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 224 optimal weight: 20.0000 chunk 348 optimal weight: 7.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 236 GLN A 331 ASN A 687 GLN A 932 GLN B 236 GLN B 331 ASN B 484 ASN B 516 HIS B 687 GLN B 954 GLN C 236 GLN C 242 HIS C 331 ASN C 687 GLN C 954 GLN C1116 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.163724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.116428 restraints weight = 30588.487| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.69 r_work: 0.3106 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.0713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31221 Z= 0.145 Angle : 0.595 10.997 42561 Z= 0.315 Chirality : 0.046 0.176 4884 Planarity : 0.004 0.079 5430 Dihedral : 6.057 56.225 4833 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.49 % Allowed : 11.17 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.13 (0.13), residues: 3822 helix: 1.90 (0.20), residues: 702 sheet: 0.25 (0.15), residues: 1002 loop : -0.60 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 630 HIS 0.005 0.001 HIS B1061 PHE 0.016 0.001 PHE B 895 TYR 0.020 0.002 TYR C1064 ARG 0.005 0.001 ARG B 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 30) link_NAG-ASN : angle 2.57834 ( 90) hydrogen bonds : bond 0.04847 ( 1325) hydrogen bonds : angle 5.95303 ( 3582) SS BOND : bond 0.00233 ( 51) SS BOND : angle 0.76731 ( 102) covalent geometry : bond 0.00325 (31140) covalent geometry : angle 0.58342 (42369) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 334 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.6038 (t0) cc_final: 0.5802 (t0) REVERT: A 391 ASN cc_start: 0.7276 (m-40) cc_final: 0.6480 (p0) REVERT: B 495 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7636 (mtt90) REVERT: B 568 ASP cc_start: 0.8300 (m-30) cc_final: 0.8069 (m-30) REVERT: B 784 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8201 (mt0) REVERT: C 316 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7964 (ttt180) REVERT: C 323 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7714 (mp) REVERT: C 331 ASN cc_start: 0.7534 (m-40) cc_final: 0.7313 (m110) REVERT: C 336 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7576 (p0) REVERT: E 59 GLU cc_start: 0.5843 (OUTLIER) cc_final: 0.5461 (mm-30) REVERT: G 11 SER cc_start: 0.7169 (OUTLIER) cc_final: 0.6847 (p) REVERT: G 26 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.6400 (mtpt) REVERT: G 87 CYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6717 (p) outliers start: 83 outliers final: 33 residues processed: 379 average time/residue: 1.3058 time to fit residues: 592.3752 Evaluate side-chains 362 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 320 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain G residue 87 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 279 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 180 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 376 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 30 optimal weight: 40.0000 chunk 153 optimal weight: 10.0000 overall best weight: 9.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 236 GLN A 331 ASN A 484 ASN A 687 GLN A 784 GLN A 932 GLN B 236 GLN B 331 ASN B 484 ASN B 687 GLN B 951 HIS B 954 GLN C 236 GLN C 242 HIS C 484 ASN C 687 GLN C 954 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.160778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.113797 restraints weight = 30556.239| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.71 r_work: 0.3050 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 31221 Z= 0.267 Angle : 0.695 7.751 42561 Z= 0.371 Chirality : 0.052 0.246 4884 Planarity : 0.005 0.066 5430 Dihedral : 6.218 59.393 4803 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.15 % Allowed : 10.96 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -0.08 (0.13), residues: 3822 helix: 1.50 (0.19), residues: 723 sheet: 0.16 (0.15), residues: 1032 loop : -0.70 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 630 HIS 0.008 0.002 HIS B1055 PHE 0.025 0.002 PHE B 895 TYR 0.022 0.003 TYR C 753 ARG 0.009 0.001 ARG C 902 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 30) link_NAG-ASN : angle 2.89111 ( 90) hydrogen bonds : bond 0.06114 ( 1325) hydrogen bonds : angle 6.10560 ( 3582) SS BOND : bond 0.00497 ( 51) SS BOND : angle 1.17667 ( 102) covalent geometry : bond 0.00616 (31140) covalent geometry : angle 0.68168 (42369) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 310 time to evaluate : 3.212 Fit side-chains REVERT: H 60 TYR cc_start: 0.6730 (m-80) cc_final: 0.6302 (m-80) REVERT: H 87 ARG cc_start: 0.5603 (OUTLIER) cc_final: 0.4873 (mmt90) REVERT: L 87 CYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6957 (p) REVERT: A 787 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8645 (mmmt) REVERT: A 1110 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8932 (mm110) REVERT: B 383 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8209 (mmmt) REVERT: B 495 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7668 (mtt90) REVERT: B 784 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8156 (mt0) REVERT: C 18 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7846 (pt) REVERT: C 316 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8067 (ttt180) REVERT: C 323 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.7895 (mp) REVERT: C 336 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7618 (p0) REVERT: C 383 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8322 (mmmt) REVERT: E 59 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5694 (mm-30) REVERT: G 11 SER cc_start: 0.7243 (OUTLIER) cc_final: 0.6832 (p) REVERT: G 26 LYS cc_start: 0.6776 (OUTLIER) cc_final: 0.6493 (mtpt) outliers start: 105 outliers final: 53 residues processed: 374 average time/residue: 1.3278 time to fit residues: 590.8039 Evaluate side-chains 374 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 306 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 26 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 243 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 193 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 368 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 chunk 233 optimal weight: 2.9990 chunk 364 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 288 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN A 185 ASN A 236 GLN A 331 ASN A 484 ASN A 687 GLN A 784 GLN A 932 GLN B 236 GLN B 331 ASN B 516 HIS B 687 GLN B 954 GLN C 236 GLN C 242 HIS C 331 ASN C 687 GLN C 954 GLN G 37 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.163449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116056 restraints weight = 30726.464| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.57 r_work: 0.3089 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31221 Z= 0.130 Angle : 0.549 6.157 42561 Z= 0.291 Chirality : 0.045 0.157 4884 Planarity : 0.004 0.058 5430 Dihedral : 5.576 57.050 4803 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.43 % Allowed : 11.59 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.16 (0.13), residues: 3822 helix: 1.88 (0.20), residues: 705 sheet: 0.22 (0.15), residues: 1032 loop : -0.55 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 630 HIS 0.004 0.001 HIS B 951 PHE 0.014 0.001 PHE B 895 TYR 0.018 0.001 TYR C1064 ARG 0.006 0.000 ARG B 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 30) link_NAG-ASN : angle 2.48416 ( 90) hydrogen bonds : bond 0.04600 ( 1325) hydrogen bonds : angle 5.71679 ( 3582) SS BOND : bond 0.00210 ( 51) SS BOND : angle 0.72339 ( 102) covalent geometry : bond 0.00287 (31140) covalent geometry : angle 0.53694 (42369) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 319 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 787 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8619 (mmmt) REVERT: B 495 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7651 (mtt90) REVERT: B 568 ASP cc_start: 0.8360 (m-30) cc_final: 0.8114 (m-30) REVERT: B 1089 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8303 (tp30) REVERT: C 18 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7875 (pt) REVERT: C 316 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7993 (ttt180) REVERT: C 323 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7744 (mp) REVERT: C 336 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7623 (p0) REVERT: C 627 THR cc_start: 0.8121 (p) cc_final: 0.7891 (t) REVERT: E 59 GLU cc_start: 0.6118 (OUTLIER) cc_final: 0.5709 (mm-30) REVERT: G 11 SER cc_start: 0.6999 (m) cc_final: 0.6623 (p) REVERT: G 26 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6529 (mtpt) REVERT: G 30 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7882 (mtpp) REVERT: G 82 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.5791 (pp20) REVERT: G 87 CYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6829 (p) outliers start: 81 outliers final: 39 residues processed: 364 average time/residue: 1.3251 time to fit residues: 573.6958 Evaluate side-chains 366 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 316 time to evaluate : 3.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 87 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 366 optimal weight: 7.9990 chunk 80 optimal weight: 0.4980 chunk 296 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 326 optimal weight: 20.0000 chunk 348 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 168 optimal weight: 0.8980 chunk 255 optimal weight: 0.8980 chunk 161 optimal weight: 20.0000 chunk 373 optimal weight: 20.0000 overall best weight: 3.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 236 GLN A 331 ASN A 484 ASN A 687 GLN A 784 GLN A 932 GLN B 185 ASN B 236 GLN B 331 ASN B 516 HIS B 687 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 HIS B 954 GLN C 236 GLN C 331 ASN C 687 GLN C 954 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.116541 restraints weight = 30633.623| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.61 r_work: 0.3091 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31221 Z= 0.123 Angle : 0.531 6.039 42561 Z= 0.282 Chirality : 0.045 0.160 4884 Planarity : 0.004 0.055 5430 Dihedral : 5.270 53.952 4802 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.52 % Allowed : 11.80 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.30 (0.13), residues: 3822 helix: 2.00 (0.20), residues: 705 sheet: 0.31 (0.15), residues: 1056 loop : -0.46 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 630 HIS 0.004 0.001 HIS B 951 PHE 0.014 0.001 PHE B 895 TYR 0.019 0.001 TYR C1064 ARG 0.007 0.000 ARG A 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 30) link_NAG-ASN : angle 2.36421 ( 90) hydrogen bonds : bond 0.04465 ( 1325) hydrogen bonds : angle 5.59090 ( 3582) SS BOND : bond 0.00196 ( 51) SS BOND : angle 0.68109 ( 102) covalent geometry : bond 0.00268 (31140) covalent geometry : angle 0.52012 (42369) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 325 time to evaluate : 3.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 83 MET cc_start: 0.6921 (mtp) cc_final: 0.5129 (mmt) REVERT: L 87 CYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6941 (p) REVERT: A 787 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8609 (mmmt) REVERT: A 1110 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8885 (mm110) REVERT: B 495 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7638 (mtt90) REVERT: B 568 ASP cc_start: 0.8278 (m-30) cc_final: 0.8063 (m-30) REVERT: B 1089 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8217 (tp30) REVERT: C 316 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7970 (ttt180) REVERT: C 323 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7742 (mp) REVERT: C 336 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7607 (p0) REVERT: C 627 THR cc_start: 0.8103 (p) cc_final: 0.7887 (t) REVERT: G 11 SER cc_start: 0.7053 (m) cc_final: 0.6752 (p) REVERT: G 26 LYS cc_start: 0.6806 (OUTLIER) cc_final: 0.6530 (mtpt) REVERT: G 30 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7846 (mtpp) REVERT: G 82 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.5788 (pp20) REVERT: G 87 CYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6777 (p) outliers start: 84 outliers final: 44 residues processed: 370 average time/residue: 1.3764 time to fit residues: 605.9418 Evaluate side-chains 372 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 317 time to evaluate : 3.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain G residue 104 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 271 optimal weight: 30.0000 chunk 218 optimal weight: 2.9990 chunk 36 optimal weight: 40.0000 chunk 381 optimal weight: 40.0000 chunk 147 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 355 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 21 optimal weight: 50.0000 chunk 191 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 236 GLN A 484 ASN A 687 GLN A 784 GLN A 932 GLN B 185 ASN B 236 GLN B 331 ASN B 484 ASN B 687 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 HIS B 954 GLN C 236 GLN C 331 ASN C 484 ASN C 655 ASN C 687 GLN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN E 29 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.161899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.114317 restraints weight = 30654.407| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.68 r_work: 0.3065 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31221 Z= 0.188 Angle : 0.598 6.681 42561 Z= 0.320 Chirality : 0.048 0.177 4884 Planarity : 0.004 0.053 5430 Dihedral : 5.567 55.046 4801 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.06 % Allowed : 11.02 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.16 (0.13), residues: 3822 helix: 1.75 (0.20), residues: 723 sheet: 0.29 (0.15), residues: 1026 loop : -0.56 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 630 HIS 0.005 0.001 HIS A1061 PHE 0.022 0.002 PHE H 68 TYR 0.021 0.002 TYR C1064 ARG 0.008 0.001 ARG A 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 30) link_NAG-ASN : angle 2.59621 ( 90) hydrogen bonds : bond 0.05239 ( 1325) hydrogen bonds : angle 5.76330 ( 3582) SS BOND : bond 0.00337 ( 51) SS BOND : angle 0.89279 ( 102) covalent geometry : bond 0.00427 (31140) covalent geometry : angle 0.58554 (42369) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 304 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 87 CYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6937 (p) REVERT: A 96 ASN cc_start: 0.7413 (m-40) cc_final: 0.6565 (t0) REVERT: A 787 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8635 (mmmt) REVERT: A 1088 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8331 (mtt-85) REVERT: A 1110 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8890 (mm110) REVERT: B 383 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8057 (mmmt) REVERT: B 495 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7646 (mtt90) REVERT: B 568 ASP cc_start: 0.8351 (m-30) cc_final: 0.8099 (m-30) REVERT: B 784 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8201 (mt0) REVERT: C 316 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8026 (ttt180) REVERT: C 323 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7837 (mp) REVERT: C 383 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8148 (mmmt) REVERT: C 627 THR cc_start: 0.8160 (p) cc_final: 0.7894 (t) REVERT: E 59 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5652 (mm-30) REVERT: G 11 SER cc_start: 0.7033 (m) cc_final: 0.6736 (p) REVERT: G 26 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6537 (mtpt) REVERT: G 30 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7893 (mtpp) REVERT: G 82 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.5878 (pp20) REVERT: G 87 CYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6799 (p) outliers start: 102 outliers final: 55 residues processed: 363 average time/residue: 1.3480 time to fit residues: 580.0445 Evaluate side-chains 375 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 305 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1088 ARG Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain G residue 104 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 378 optimal weight: 20.0000 chunk 359 optimal weight: 3.9990 chunk 102 optimal weight: 30.0000 chunk 29 optimal weight: 0.0570 chunk 32 optimal weight: 30.0000 chunk 3 optimal weight: 20.0000 chunk 249 optimal weight: 3.9990 chunk 264 optimal weight: 10.0000 chunk 311 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 233 optimal weight: 10.0000 overall best weight: 5.6110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 204 HIS A 236 GLN A 484 ASN A 687 GLN A 784 GLN A 932 GLN B 185 ASN B 236 GLN B 331 ASN B 484 ASN B 687 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 HIS B 954 GLN B1116 ASN C 236 GLN C 331 ASN C 484 ASN C 687 GLN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN E 29 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.162041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112517 restraints weight = 30439.051| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.65 r_work: 0.3067 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31221 Z= 0.174 Angle : 0.585 7.030 42561 Z= 0.312 Chirality : 0.047 0.201 4884 Planarity : 0.004 0.051 5430 Dihedral : 5.544 58.174 4801 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.94 % Allowed : 11.44 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.17 (0.13), residues: 3822 helix: 1.75 (0.20), residues: 723 sheet: 0.32 (0.15), residues: 1026 loop : -0.56 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 630 HIS 0.005 0.001 HIS A1061 PHE 0.019 0.002 PHE H 68 TYR 0.020 0.002 TYR C1064 ARG 0.007 0.000 ARG A 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 30) link_NAG-ASN : angle 2.59953 ( 90) hydrogen bonds : bond 0.05061 ( 1325) hydrogen bonds : angle 5.72792 ( 3582) SS BOND : bond 0.00305 ( 51) SS BOND : angle 0.82590 ( 102) covalent geometry : bond 0.00394 (31140) covalent geometry : angle 0.57246 (42369) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 309 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 87 CYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6951 (p) REVERT: A 96 ASN cc_start: 0.7386 (m-40) cc_final: 0.6543 (t0) REVERT: A 787 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8613 (mmmt) REVERT: A 1110 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8919 (mm110) REVERT: B 495 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7621 (mtt90) REVERT: B 568 ASP cc_start: 0.8315 (m-30) cc_final: 0.8067 (m-30) REVERT: B 784 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8216 (mt0) REVERT: C 316 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7968 (ttt180) REVERT: C 323 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7817 (mp) REVERT: C 336 ASP cc_start: 0.7703 (p0) cc_final: 0.7446 (OUTLIER) REVERT: C 383 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8065 (mmmt) REVERT: C 627 THR cc_start: 0.8097 (p) cc_final: 0.7831 (t) REVERT: E 59 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5616 (mm-30) REVERT: G 11 SER cc_start: 0.7108 (m) cc_final: 0.6803 (p) REVERT: G 26 LYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6507 (mtpt) REVERT: G 30 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7845 (mtpp) REVERT: G 82 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.5874 (pp20) REVERT: G 87 CYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6797 (p) outliers start: 98 outliers final: 58 residues processed: 364 average time/residue: 1.3358 time to fit residues: 581.5734 Evaluate side-chains 374 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 304 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain G residue 104 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 240 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 254 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 379 optimal weight: 0.8980 chunk 291 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 296 optimal weight: 7.9990 chunk 376 optimal weight: 40.0000 chunk 101 optimal weight: 0.0020 chunk 9 optimal weight: 5.9990 overall best weight: 3.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 204 HIS A 236 GLN A 687 GLN A 784 GLN A 932 GLN B 236 GLN B 331 ASN B 687 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN B 954 GLN C 236 GLN C 331 ASN C 687 GLN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN E 29 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.114333 restraints weight = 30631.804| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.67 r_work: 0.3085 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31221 Z= 0.141 Angle : 0.551 7.029 42561 Z= 0.293 Chirality : 0.045 0.167 4884 Planarity : 0.004 0.051 5430 Dihedral : 5.313 59.375 4799 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.55 % Allowed : 11.83 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.30 (0.13), residues: 3822 helix: 1.97 (0.20), residues: 705 sheet: 0.36 (0.15), residues: 1026 loop : -0.47 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 630 HIS 0.004 0.001 HIS B1061 PHE 0.016 0.001 PHE B 895 TYR 0.019 0.002 TYR C1064 ARG 0.007 0.000 ARG A 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 30) link_NAG-ASN : angle 2.55208 ( 90) hydrogen bonds : bond 0.04672 ( 1325) hydrogen bonds : angle 5.61364 ( 3582) SS BOND : bond 0.00229 ( 51) SS BOND : angle 0.71078 ( 102) covalent geometry : bond 0.00314 (31140) covalent geometry : angle 0.53857 (42369) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 312 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 87 CYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6952 (p) REVERT: A 96 ASN cc_start: 0.7441 (m-40) cc_final: 0.6650 (t0) REVERT: A 787 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8620 (mmmt) REVERT: A 1110 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8903 (mm110) REVERT: B 383 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8113 (mmmt) REVERT: B 495 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7642 (mtt90) REVERT: B 568 ASP cc_start: 0.8305 (m-30) cc_final: 0.8080 (m-30) REVERT: C 316 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7990 (ttt180) REVERT: C 323 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7769 (mp) REVERT: C 336 ASP cc_start: 0.7762 (p0) cc_final: 0.7510 (p0) REVERT: C 627 THR cc_start: 0.8105 (p) cc_final: 0.7889 (t) REVERT: C 851 LYS cc_start: 0.8879 (ttmm) cc_final: 0.8311 (mmtm) REVERT: G 11 SER cc_start: 0.7075 (m) cc_final: 0.6787 (p) REVERT: G 26 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6512 (mtpt) REVERT: G 30 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7843 (mtpp) REVERT: G 82 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.5916 (pp20) REVERT: G 87 CYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6758 (p) outliers start: 85 outliers final: 51 residues processed: 359 average time/residue: 1.3033 time to fit residues: 558.6874 Evaluate side-chains 372 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 310 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain G residue 104 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 41 optimal weight: 10.0000 chunk 363 optimal weight: 8.9990 chunk 208 optimal weight: 0.9990 chunk 210 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 260 optimal weight: 9.9990 chunk 327 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 283 optimal weight: 6.9990 chunk 309 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 236 GLN A 784 GLN A 932 GLN B 236 GLN B 331 ASN B 687 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 HIS B 954 GLN C 236 GLN C 331 ASN C 687 GLN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN E 29 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.162793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116348 restraints weight = 30609.467| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.62 r_work: 0.3088 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31221 Z= 0.141 Angle : 0.553 7.695 42561 Z= 0.294 Chirality : 0.046 0.174 4884 Planarity : 0.004 0.051 5430 Dihedral : 5.261 59.703 4799 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.49 % Allowed : 12.01 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.28 (0.13), residues: 3822 helix: 1.96 (0.20), residues: 705 sheet: 0.37 (0.15), residues: 1023 loop : -0.50 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 630 HIS 0.006 0.001 HIS B 951 PHE 0.016 0.001 PHE B 895 TYR 0.019 0.002 TYR C1064 ARG 0.008 0.000 ARG B 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 30) link_NAG-ASN : angle 2.64720 ( 90) hydrogen bonds : bond 0.04702 ( 1325) hydrogen bonds : angle 5.59489 ( 3582) SS BOND : bond 0.00232 ( 51) SS BOND : angle 0.71367 ( 102) covalent geometry : bond 0.00315 (31140) covalent geometry : angle 0.53977 (42369) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 306 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 87 CYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6951 (p) REVERT: A 96 ASN cc_start: 0.7360 (m-40) cc_final: 0.6589 (t0) REVERT: A 787 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8615 (mmmt) REVERT: A 1110 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8904 (mm110) REVERT: B 383 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8111 (mmmt) REVERT: B 495 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7652 (mtt90) REVERT: B 568 ASP cc_start: 0.8281 (m-30) cc_final: 0.8046 (m-30) REVERT: C 316 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7994 (ttt180) REVERT: C 323 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7770 (mp) REVERT: C 336 ASP cc_start: 0.7788 (p0) cc_final: 0.7548 (p0) REVERT: C 627 THR cc_start: 0.8127 (p) cc_final: 0.7917 (t) REVERT: C 851 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8318 (mmtm) REVERT: G 11 SER cc_start: 0.7106 (m) cc_final: 0.6818 (p) REVERT: G 26 LYS cc_start: 0.6794 (OUTLIER) cc_final: 0.6529 (mtpt) REVERT: G 30 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7844 (mtpp) REVERT: G 82 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.5905 (pp20) REVERT: G 87 CYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6742 (p) outliers start: 83 outliers final: 55 residues processed: 352 average time/residue: 1.3794 time to fit residues: 579.9292 Evaluate side-chains 372 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 306 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain G residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 73 optimal weight: 0.9980 chunk 300 optimal weight: 20.0000 chunk 12 optimal weight: 50.0000 chunk 78 optimal weight: 7.9990 chunk 54 optimal weight: 0.0370 chunk 340 optimal weight: 1.9990 chunk 285 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 294 optimal weight: 20.0000 chunk 225 optimal weight: 5.9990 overall best weight: 3.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 236 GLN A 784 GLN A 932 GLN B 236 GLN B 331 ASN B 687 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 236 GLN C 331 ASN C 687 GLN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN E 29 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.163132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116386 restraints weight = 30633.953| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.76 r_work: 0.3084 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31221 Z= 0.129 Angle : 0.540 8.034 42561 Z= 0.287 Chirality : 0.045 0.160 4884 Planarity : 0.004 0.051 5430 Dihedral : 5.139 58.796 4798 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.40 % Allowed : 12.07 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.34 (0.13), residues: 3822 helix: 1.99 (0.20), residues: 705 sheet: 0.43 (0.15), residues: 993 loop : -0.46 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 630 HIS 0.003 0.001 HIS B1061 PHE 0.015 0.001 PHE B 895 TYR 0.018 0.001 TYR C1064 ARG 0.007 0.000 ARG A 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 30) link_NAG-ASN : angle 2.50062 ( 90) hydrogen bonds : bond 0.04512 ( 1325) hydrogen bonds : angle 5.53768 ( 3582) SS BOND : bond 0.00201 ( 51) SS BOND : angle 0.66768 ( 102) covalent geometry : bond 0.00285 (31140) covalent geometry : angle 0.52760 (42369) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 312 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 83 MET cc_start: 0.6936 (mtp) cc_final: 0.6714 (mtm) REVERT: H 58 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7660 (m) REVERT: L 87 CYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6925 (p) REVERT: A 96 ASN cc_start: 0.7447 (m-40) cc_final: 0.6701 (t0) REVERT: A 336 ASP cc_start: 0.7928 (p0) cc_final: 0.7657 (p0) REVERT: A 787 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8632 (mmmt) REVERT: A 1088 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8332 (mtt-85) REVERT: A 1110 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8917 (mm110) REVERT: B 383 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8101 (mmmt) REVERT: B 495 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7643 (mtt90) REVERT: B 534 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8299 (mtmt) REVERT: B 568 ASP cc_start: 0.8266 (m-30) cc_final: 0.8040 (m-30) REVERT: C 316 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7978 (ttt180) REVERT: C 323 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7757 (mp) REVERT: C 336 ASP cc_start: 0.7782 (p0) cc_final: 0.7533 (p0) REVERT: C 383 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8084 (mmmt) REVERT: C 851 LYS cc_start: 0.8886 (ttmm) cc_final: 0.8312 (mmtm) REVERT: G 11 SER cc_start: 0.7100 (m) cc_final: 0.6813 (p) REVERT: G 26 LYS cc_start: 0.6739 (OUTLIER) cc_final: 0.6473 (mtpt) REVERT: G 30 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7801 (mtpp) REVERT: G 82 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.5802 (pp20) REVERT: G 87 CYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6723 (p) outliers start: 80 outliers final: 53 residues processed: 355 average time/residue: 1.3300 time to fit residues: 560.7002 Evaluate side-chains 377 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 310 time to evaluate : 4.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1088 ARG Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain G residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 190 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 178 optimal weight: 10.0000 chunk 359 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 chunk 324 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 236 GLN A 784 GLN A 932 GLN B 236 GLN B 331 ASN B 687 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 HIS B 954 GLN C 236 GLN C 331 ASN C 687 GLN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN E 29 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.162593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116729 restraints weight = 30637.544| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.75 r_work: 0.3077 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31221 Z= 0.148 Angle : 0.558 7.694 42561 Z= 0.297 Chirality : 0.046 0.167 4884 Planarity : 0.004 0.051 5430 Dihedral : 5.220 58.356 4798 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.43 % Allowed : 12.04 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.25 (0.13), residues: 3822 helix: 1.80 (0.20), residues: 723 sheet: 0.43 (0.15), residues: 993 loop : -0.53 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 630 HIS 0.005 0.001 HIS B 951 PHE 0.017 0.002 PHE B 895 TYR 0.020 0.002 TYR B 393 ARG 0.006 0.000 ARG A 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 30) link_NAG-ASN : angle 2.53769 ( 90) hydrogen bonds : bond 0.04776 ( 1325) hydrogen bonds : angle 5.59500 ( 3582) SS BOND : bond 0.00245 ( 51) SS BOND : angle 0.74385 ( 102) covalent geometry : bond 0.00331 (31140) covalent geometry : angle 0.54537 (42369) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31661.36 seconds wall clock time: 545 minutes 24.82 seconds (32724.82 seconds total)