Starting phenix.real_space_refine on Wed Jun 25 19:41:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r1d_18808/06_2025/8r1d_18808.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r1d_18808/06_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_18808/06_2025/8r1d_18808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r1d_18808/06_2025/8r1d_18808.map" model { file = "/net/cci-nas-00/data/ceres_data/8r1d_18808/06_2025/8r1d_18808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r1d_18808/06_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): 0.42s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 17.38, per 1000 atoms: 0.57 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: 7.88 Conformation dependent library (CDL) restraints added in 3.7 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: 5.08 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: 15.59 Time building geometry restraints manager: 8.83 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: 0.680 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: 1.390 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 71.890 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.640 ------------------------------------------------------------------------------- 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 : 3.201 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: 1.3603 time to fit residues: 581.7873 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 : 3.570 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.163715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.117159 restraints weight = 30592.845| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.69 r_work: 0.3096 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 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 56.227 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 0.00283 ( 30) link_NAG-ASN : angle 2.57801 ( 90) hydrogen bonds : bond 0.04848 ( 1325) hydrogen bonds : angle 5.95297 ( 3582) SS BOND : bond 0.00233 ( 51) SS BOND : angle 0.76748 ( 102) covalent geometry : bond 0.00325 (31140) covalent geometry : angle 0.58340 (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 : 2.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.6048 (t0) cc_final: 0.5807 (t0) REVERT: A 391 ASN cc_start: 0.7274 (m-40) cc_final: 0.6470 (p0) REVERT: B 495 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7631 (mtt90) REVERT: B 568 ASP cc_start: 0.8307 (m-30) cc_final: 0.8077 (m-30) REVERT: B 784 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8211 (mt0) REVERT: C 316 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7981 (ttt180) REVERT: C 323 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7717 (mp) REVERT: C 331 ASN cc_start: 0.7541 (m-40) cc_final: 0.7317 (m110) REVERT: C 336 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7560 (p0) REVERT: E 59 GLU cc_start: 0.5850 (OUTLIER) cc_final: 0.5469 (mm-30) REVERT: G 11 SER cc_start: 0.7165 (OUTLIER) cc_final: 0.6842 (p) REVERT: G 26 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.6402 (mtpt) REVERT: G 87 CYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6754 (p) outliers start: 83 outliers final: 33 residues processed: 379 average time/residue: 1.3030 time to fit residues: 590.5159 Evaluate side-chains 363 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 321 time to evaluate : 3.256 ------------------------------------------------------------------------------- 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: 9.9990 chunk 88 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 180 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 376 optimal weight: 40.0000 chunk 236 optimal weight: 9.9990 chunk 30 optimal weight: 30.0000 chunk 153 optimal weight: 10.0000 overall best weight: 11.9996 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.160077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.113612 restraints weight = 30580.861| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.79 r_work: 0.3041 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 31221 Z= 0.324 Angle : 0.751 8.142 42561 Z= 0.402 Chirality : 0.055 0.291 4884 Planarity : 0.005 0.064 5430 Dihedral : 6.464 59.858 4803 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.42 % Allowed : 10.69 % 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: -0.15 (0.13), residues: 3822 helix: 1.42 (0.19), residues: 723 sheet: 0.14 (0.15), residues: 1053 loop : -0.76 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 630 HIS 0.009 0.002 HIS A1055 PHE 0.027 0.003 PHE B 895 TYR 0.024 0.003 TYR C 753 ARG 0.011 0.001 ARG C 902 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 30) link_NAG-ASN : angle 3.08016 ( 90) hydrogen bonds : bond 0.06455 ( 1325) hydrogen bonds : angle 6.17725 ( 3582) SS BOND : bond 0.00604 ( 51) SS BOND : angle 1.35654 ( 102) covalent geometry : bond 0.00751 (31140) covalent geometry : angle 0.73629 (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 426 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 312 time to evaluate : 3.054 Fit side-chains REVERT: H 38 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6037 (ptt-90) REVERT: H 87 ARG cc_start: 0.5607 (OUTLIER) cc_final: 0.4917 (mmt90) REVERT: A 787 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8644 (mmmt) REVERT: A 1110 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8925 (mm110) REVERT: B 495 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7697 (mtt90) REVERT: B 784 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: C 18 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7808 (pt) REVERT: C 316 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8085 (ttt180) REVERT: C 323 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.7907 (mp) REVERT: C 336 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7654 (p0) REVERT: C 383 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8445 (mmmt) REVERT: E 59 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5739 (mm-30) REVERT: G 11 SER cc_start: 0.7180 (OUTLIER) cc_final: 0.6753 (p) REVERT: G 26 LYS cc_start: 0.6796 (OUTLIER) cc_final: 0.6521 (mtpt) outliers start: 114 outliers final: 58 residues processed: 382 average time/residue: 1.4002 time to fit residues: 636.4332 Evaluate side-chains 377 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 305 time to evaluate : 3.494 ------------------------------------------------------------------------------- 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 F residue 70 ILE Chi-restraints excluded: chain H residue 38 ARG 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 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 569 THR 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 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 569 THR 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 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 758 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: 0.9980 chunk 11 optimal weight: 4.9990 chunk 193 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 368 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 233 optimal weight: 3.9990 chunk 364 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 288 optimal weight: 5.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 954 GLN C 236 GLN C 242 HIS C 331 ASN C 687 GLN C 910 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 = 0.3852 r_free = 0.3852 target = 0.163098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123802 restraints weight = 30672.528| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.16 r_work: 0.3147 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31221 Z= 0.131 Angle : 0.558 6.317 42561 Z= 0.296 Chirality : 0.045 0.160 4884 Planarity : 0.004 0.057 5430 Dihedral : 5.745 56.982 4803 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.64 % Allowed : 11.29 % Favored : 86.07 % 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: 0.11 (0.13), residues: 3822 helix: 1.84 (0.20), residues: 705 sheet: 0.21 (0.15), residues: 996 loop : -0.57 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 630 HIS 0.004 0.001 HIS B1061 PHE 0.015 0.001 PHE B 895 TYR 0.018 0.002 TYR C1064 ARG 0.006 0.000 ARG A 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 30) link_NAG-ASN : angle 2.56695 ( 90) hydrogen bonds : bond 0.04677 ( 1325) hydrogen bonds : angle 5.77278 ( 3582) SS BOND : bond 0.00215 ( 51) SS BOND : angle 0.76515 ( 102) covalent geometry : bond 0.00286 (31140) covalent geometry : angle 0.54550 (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 409 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 321 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 83 MET cc_start: 0.6905 (mtp) cc_final: 0.5210 (mmt) REVERT: A 787 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8568 (mmmt) REVERT: A 1088 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8272 (mtt-85) REVERT: B 495 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7682 (mtt90) REVERT: B 568 ASP cc_start: 0.8304 (m-30) cc_final: 0.8039 (m-30) REVERT: B 1089 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8132 (tp30) REVERT: C 18 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7880 (pt) REVERT: C 316 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7844 (ttt180) REVERT: C 323 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7761 (mp) REVERT: C 627 THR cc_start: 0.8104 (p) cc_final: 0.7866 (t) REVERT: E 59 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.5655 (mm-30) REVERT: G 11 SER cc_start: 0.7009 (m) cc_final: 0.6616 (p) REVERT: G 26 LYS cc_start: 0.6806 (OUTLIER) cc_final: 0.6562 (mtpt) REVERT: G 82 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.5950 (pp20) REVERT: G 87 CYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6751 (p) outliers start: 88 outliers final: 46 residues processed: 373 average time/residue: 1.3754 time to fit residues: 609.0712 Evaluate side-chains 368 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 312 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 VAL 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 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 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 1088 ARG 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 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 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 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 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 782 VAL 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 59 GLU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain G residue 26 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 366 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 296 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 326 optimal weight: 20.0000 chunk 348 optimal weight: 10.0000 chunk 214 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 255 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 373 optimal weight: 30.0000 overall best weight: 3.4784 ------------------------------------------------------------------------------- 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 185 ASN B 236 GLN B 331 ASN B 484 ASN B 516 HIS 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 954 GLN G 37 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.163147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.115992 restraints weight = 30590.759| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.59 r_work: 0.3094 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1131 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= 0.131 Angle : 0.545 5.981 42561 Z= 0.290 Chirality : 0.045 0.162 4884 Planarity : 0.004 0.055 5430 Dihedral : 5.445 55.716 4801 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.61 % Allowed : 11.47 % 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: 0.25 (0.13), residues: 3822 helix: 1.95 (0.20), residues: 705 sheet: 0.26 (0.15), residues: 1026 loop : -0.48 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 630 HIS 0.004 0.001 HIS A1061 PHE 0.019 0.001 PHE H 68 TYR 0.019 0.002 TYR C1064 ARG 0.007 0.000 ARG B 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 30) link_NAG-ASN : angle 2.41794 ( 90) hydrogen bonds : bond 0.04614 ( 1325) hydrogen bonds : angle 5.65198 ( 3582) SS BOND : bond 0.00221 ( 51) SS BOND : angle 0.75780 ( 102) covalent geometry : bond 0.00289 (31140) covalent geometry : angle 0.53310 (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 408 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 321 time to evaluate : 3.306 Fit side-chains revert: symmetry clash REVERT: A 787 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8620 (mmmt) REVERT: A 1110 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8864 (mm110) REVERT: B 495 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7668 (mtt90) REVERT: B 568 ASP cc_start: 0.8298 (m-30) cc_final: 0.8066 (m-30) REVERT: B 1089 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8234 (tp30) REVERT: C 316 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7991 (ttt180) REVERT: C 323 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7772 (mp) REVERT: C 336 ASP cc_start: 0.7652 (p0) cc_final: 0.7414 (OUTLIER) REVERT: C 627 THR cc_start: 0.8133 (p) cc_final: 0.7911 (t) REVERT: C 1088 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8240 (mtt-85) REVERT: E 59 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5633 (mm-30) REVERT: G 11 SER cc_start: 0.7007 (m) cc_final: 0.6685 (p) REVERT: G 26 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6542 (mtpt) REVERT: G 30 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7872 (mtpp) REVERT: G 82 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.5861 (pp20) REVERT: G 87 CYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6766 (p) outliers start: 87 outliers final: 46 residues processed: 369 average time/residue: 1.4104 time to fit residues: 621.4018 Evaluate side-chains 371 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 315 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F 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 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 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 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 1088 ARG 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 271 optimal weight: 40.0000 chunk 218 optimal weight: 6.9990 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: 10.0000 chunk 59 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 chunk 191 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 overall best weight: 10.5994 ------------------------------------------------------------------------------- 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 331 ASN A 484 ASN A 687 GLN A 784 GLN A 932 GLN B 236 GLN B 331 ASN B 484 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 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.160224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.112865 restraints weight = 30623.406| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.64 r_work: 0.3035 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 31221 Z= 0.290 Angle : 0.702 7.194 42561 Z= 0.376 Chirality : 0.053 0.257 4884 Planarity : 0.005 0.059 5430 Dihedral : 6.156 59.357 4801 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.27 % Allowed : 11.14 % Favored : 85.59 % 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: -0.03 (0.13), residues: 3822 helix: 1.57 (0.20), residues: 723 sheet: 0.16 (0.15), residues: 1047 loop : -0.67 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 630 HIS 0.008 0.002 HIS A1061 PHE 0.026 0.003 PHE B 895 TYR 0.023 0.003 TYR B 393 ARG 0.010 0.001 ARG C 902 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 30) link_NAG-ASN : angle 2.83114 ( 90) hydrogen bonds : bond 0.06092 ( 1325) hydrogen bonds : angle 6.00031 ( 3582) SS BOND : bond 0.00543 ( 51) SS BOND : angle 1.30696 ( 102) covalent geometry : bond 0.00673 (31140) covalent geometry : angle 0.68801 (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 417 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 308 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 83 MET cc_start: 0.6932 (mtp) cc_final: 0.6678 (mtm) REVERT: D 38 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6735 (ptt-90) REVERT: A 787 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8637 (mmmt) REVERT: A 1088 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8310 (mtt-85) REVERT: A 1110 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8943 (mm110) REVERT: B 383 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8228 (mmmt) REVERT: B 495 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7658 (mtt90) REVERT: B 784 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8207 (mt0) REVERT: C 316 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8044 (ttt180) REVERT: C 323 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7905 (mp) REVERT: C 336 ASP cc_start: 0.7773 (p0) cc_final: 0.7528 (p0) REVERT: C 383 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8393 (mmmt) REVERT: E 59 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5670 (mm-30) REVERT: G 26 LYS cc_start: 0.6822 (OUTLIER) cc_final: 0.6594 (mtpt) REVERT: G 30 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7897 (mtpp) REVERT: G 82 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.5926 (pp20) REVERT: G 87 CYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6876 (p) outliers start: 109 outliers final: 57 residues processed: 376 average time/residue: 1.4195 time to fit residues: 633.5531 Evaluate side-chains 382 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 310 time to evaluate : 3.036 ------------------------------------------------------------------------------- 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 F residue 70 ILE Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 73 THR 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 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 1088 ARG 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 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 92 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 782 VAL 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 824 THR Chi-restraints excluded: chain C residue 836 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 378 optimal weight: 20.0000 chunk 359 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 249 optimal weight: 10.0000 chunk 264 optimal weight: 30.0000 chunk 311 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 236 GLN B 331 ASN B 484 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 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.161126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.112435 restraints weight = 30352.842| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.70 r_work: 0.3027 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31221 Z= 0.208 Angle : 0.625 6.601 42561 Z= 0.334 Chirality : 0.049 0.205 4884 Planarity : 0.004 0.053 5430 Dihedral : 5.970 59.944 4801 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.03 % Allowed : 11.65 % Favored : 85.32 % 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: -0.01 (0.13), residues: 3822 helix: 1.63 (0.20), residues: 723 sheet: 0.16 (0.15), residues: 1077 loop : -0.68 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 630 HIS 0.006 0.001 HIS A1061 PHE 0.021 0.002 PHE B 895 TYR 0.021 0.002 TYR B 393 ARG 0.007 0.001 ARG A 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 30) link_NAG-ASN : angle 2.74031 ( 90) hydrogen bonds : bond 0.05423 ( 1325) hydrogen bonds : angle 5.87505 ( 3582) SS BOND : bond 0.00368 ( 51) SS BOND : angle 0.99064 ( 102) covalent geometry : bond 0.00475 (31140) covalent geometry : angle 0.61211 (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: 101 poor density : 306 time to evaluate : 3.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 87 ARG cc_start: 0.5479 (OUTLIER) cc_final: 0.4789 (mmt90) REVERT: A 96 ASN cc_start: 0.7408 (m-40) cc_final: 0.6546 (t0) REVERT: A 787 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8644 (mmmt) REVERT: A 1088 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8394 (mtt-85) REVERT: A 1110 GLN cc_start: 0.9216 (OUTLIER) cc_final: 0.8971 (mm110) REVERT: B 383 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8100 (mmmt) REVERT: B 495 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7639 (mtt90) REVERT: B 568 ASP cc_start: 0.8347 (m-30) cc_final: 0.8090 (m-30) REVERT: B 784 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: C 316 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8049 (ttt180) REVERT: C 323 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7872 (mp) REVERT: C 336 ASP cc_start: 0.7780 (p0) cc_final: 0.7527 (p0) REVERT: C 383 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8179 (mmmt) REVERT: C 627 THR cc_start: 0.8102 (p) cc_final: 0.7824 (t) REVERT: E 59 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5612 (mm-30) REVERT: G 26 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6548 (mtpt) REVERT: G 30 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7907 (mtpp) REVERT: G 82 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6342 (mm-30) REVERT: G 87 CYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6810 (p) outliers start: 101 outliers final: 60 residues processed: 366 average time/residue: 1.4946 time to fit residues: 655.6853 Evaluate side-chains 380 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 305 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 73 THR 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 320 THR Chi-restraints excluded: chain A residue 364 VAL 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 721 THR 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 A residue 1130 VAL 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 92 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 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 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 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 21 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: 6.9990 chunk 8 optimal weight: 1.9990 chunk 254 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 379 optimal weight: 20.0000 chunk 291 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 296 optimal weight: 20.0000 chunk 376 optimal weight: 40.0000 chunk 101 optimal weight: 5.9990 chunk 9 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 687 GLN A 784 GLN A 932 GLN 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 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 = 0.3839 r_free = 0.3839 target = 0.161967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113283 restraints weight = 30656.180| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.57 r_work: 0.3072 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31221 Z= 0.159 Angle : 0.577 6.890 42561 Z= 0.308 Chirality : 0.046 0.190 4884 Planarity : 0.004 0.054 5430 Dihedral : 5.700 59.538 4799 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.70 % Allowed : 11.98 % Favored : 85.32 % 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: 0.10 (0.13), residues: 3822 helix: 1.74 (0.20), residues: 723 sheet: 0.23 (0.15), residues: 1047 loop : -0.61 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 630 HIS 0.006 0.001 HIS B 951 PHE 0.017 0.002 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 0.00291 ( 30) link_NAG-ASN : angle 2.62058 ( 90) hydrogen bonds : bond 0.04937 ( 1325) hydrogen bonds : angle 5.73667 ( 3582) SS BOND : bond 0.00268 ( 51) SS BOND : angle 0.81981 ( 102) covalent geometry : bond 0.00358 (31140) covalent geometry : angle 0.56445 (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 401 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 311 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.7378 (m-40) cc_final: 0.6588 (t0) REVERT: A 787 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8629 (mmmt) REVERT: A 1088 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8330 (mtt-85) REVERT: A 1110 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8912 (mm110) REVERT: B 495 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7690 (mtt90) REVERT: B 568 ASP cc_start: 0.8321 (m-30) cc_final: 0.8078 (m-30) REVERT: C 316 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7971 (ttt180) REVERT: C 323 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7821 (mp) REVERT: C 336 ASP cc_start: 0.7816 (p0) cc_final: 0.7554 (p0) REVERT: C 627 THR cc_start: 0.8117 (p) cc_final: 0.7871 (t) REVERT: E 59 GLU cc_start: 0.6006 (OUTLIER) cc_final: 0.5558 (mm-30) REVERT: G 26 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6538 (mtpt) REVERT: G 30 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7926 (mtpp) REVERT: G 82 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.5933 (pp20) REVERT: G 87 CYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6759 (p) outliers start: 90 outliers final: 55 residues processed: 363 average time/residue: 1.4393 time to fit residues: 620.5831 Evaluate side-chains 373 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 307 time to evaluate : 3.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 73 THR 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 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 721 THR 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 20 THR 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 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 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 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 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 21 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 41 optimal weight: 0.8980 chunk 363 optimal weight: 8.9990 chunk 208 optimal weight: 8.9990 chunk 210 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 260 optimal weight: 4.9990 chunk 327 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 299 optimal weight: 10.0000 chunk 283 optimal weight: 7.9990 chunk 309 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 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 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.161840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.114994 restraints weight = 30532.925| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.69 r_work: 0.3072 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31221 Z= 0.168 Angle : 0.586 7.383 42561 Z= 0.313 Chirality : 0.047 0.180 4884 Planarity : 0.004 0.053 5430 Dihedral : 5.669 58.778 4799 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.67 % Allowed : 11.98 % Favored : 85.35 % 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: 1.73 (0.20), residues: 723 sheet: 0.26 (0.15), residues: 1023 loop : -0.64 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 630 HIS 0.005 0.001 HIS B 951 PHE 0.018 0.002 PHE B 895 TYR 0.021 0.002 TYR B 393 ARG 0.006 0.000 ARG A 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 30) link_NAG-ASN : angle 2.70708 ( 90) hydrogen bonds : bond 0.05049 ( 1325) hydrogen bonds : angle 5.73423 ( 3582) SS BOND : bond 0.00289 ( 51) SS BOND : angle 0.85846 ( 102) covalent geometry : bond 0.00378 (31140) covalent geometry : angle 0.57284 (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 393 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 304 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 87 ARG cc_start: 0.5535 (OUTLIER) cc_final: 0.4829 (mmt90) REVERT: A 96 ASN cc_start: 0.7347 (m-40) cc_final: 0.6610 (t0) REVERT: A 787 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8620 (mmmt) REVERT: A 1088 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8349 (mtt-85) REVERT: A 1110 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8921 (mm110) REVERT: B 383 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8111 (mmmt) REVERT: B 495 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7675 (mtt90) REVERT: B 568 ASP cc_start: 0.8269 (m-30) cc_final: 0.8004 (m-30) REVERT: C 316 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7990 (ttt180) REVERT: C 323 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7824 (mp) REVERT: C 336 ASP cc_start: 0.7818 (p0) cc_final: 0.7527 (p0) REVERT: C 383 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8189 (mmmt) REVERT: C 627 THR cc_start: 0.8117 (p) cc_final: 0.7867 (t) REVERT: E 59 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5563 (mm-30) REVERT: G 26 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.6561 (mtpt) REVERT: G 30 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7899 (mtpp) REVERT: G 82 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.5922 (pp20) REVERT: G 87 CYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6763 (p) outliers start: 89 outliers final: 59 residues processed: 356 average time/residue: 1.4866 time to fit residues: 634.4545 Evaluate side-chains 378 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 305 time to evaluate : 3.758 ------------------------------------------------------------------------------- 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 H residue 87 ARG Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 73 THR 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 721 THR 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 20 THR 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 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 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 617 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 230 ILE 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 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 17 THR Chi-restraints excluded: chain G residue 21 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 73 optimal weight: 0.6980 chunk 300 optimal weight: 20.0000 chunk 12 optimal weight: 50.0000 chunk 78 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 340 optimal weight: 7.9990 chunk 285 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 225 optimal weight: 6.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- 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 784 GLN A 932 GLN B 236 GLN B 331 ASN B 484 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 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN E 29 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.162530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.114178 restraints weight = 30468.523| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.62 r_work: 0.3062 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31221 Z= 0.166 Angle : 0.582 7.780 42561 Z= 0.310 Chirality : 0.047 0.172 4884 Planarity : 0.004 0.053 5430 Dihedral : 5.606 58.645 4799 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.46 % Allowed : 12.22 % Favored : 85.32 % 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: 0.09 (0.13), residues: 3822 helix: 1.73 (0.20), residues: 723 sheet: 0.27 (0.15), residues: 1023 loop : -0.63 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 630 HIS 0.005 0.001 HIS A1061 PHE 0.018 0.002 PHE B 895 TYR 0.022 0.002 TYR B 393 ARG 0.009 0.000 ARG B 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 30) link_NAG-ASN : angle 2.64625 ( 90) hydrogen bonds : bond 0.04991 ( 1325) hydrogen bonds : angle 5.71571 ( 3582) SS BOND : bond 0.00283 ( 51) SS BOND : angle 0.83752 ( 102) covalent geometry : bond 0.00374 (31140) covalent geometry : angle 0.56924 (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 387 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 305 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 87 ARG cc_start: 0.5504 (OUTLIER) cc_final: 0.4799 (mmt90) REVERT: A 96 ASN cc_start: 0.7386 (m-40) cc_final: 0.6615 (t0) REVERT: A 336 ASP cc_start: 0.7915 (p0) cc_final: 0.7649 (p0) REVERT: A 787 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8647 (mmmt) REVERT: A 1088 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8344 (mtt-85) REVERT: A 1110 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8940 (mm110) REVERT: B 383 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8064 (mmmt) REVERT: B 495 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7663 (mtt90) REVERT: B 568 ASP cc_start: 0.8298 (m-30) cc_final: 0.8067 (m-30) REVERT: C 316 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8007 (ttt180) REVERT: C 323 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7830 (mp) REVERT: C 336 ASP cc_start: 0.7863 (p0) cc_final: 0.7571 (p0) REVERT: C 383 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8190 (mmmt) REVERT: C 627 THR cc_start: 0.8119 (p) cc_final: 0.7871 (t) REVERT: E 59 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5548 (mm-30) REVERT: G 26 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6555 (mtpt) REVERT: G 30 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7877 (mtpp) REVERT: G 82 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.5929 (pp20) REVERT: G 87 CYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6774 (p) outliers start: 82 outliers final: 56 residues processed: 352 average time/residue: 1.3589 time to fit residues: 567.5721 Evaluate side-chains 373 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 303 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 73 THR 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 721 THR 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 20 THR 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 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 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 617 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 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 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 17 THR Chi-restraints excluded: chain G residue 21 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 190 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 20 optimal weight: 30.0000 chunk 13 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 chunk 359 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 324 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 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 687 GLN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN E 29 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.161185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.112795 restraints weight = 30635.748| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.68 r_work: 0.3066 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31221 Z= 0.167 Angle : 0.585 7.944 42561 Z= 0.312 Chirality : 0.047 0.172 4884 Planarity : 0.004 0.053 5430 Dihedral : 5.584 58.768 4799 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.58 % Allowed : 12.19 % Favored : 85.23 % 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: 1.73 (0.20), residues: 723 sheet: 0.23 (0.15), residues: 1047 loop : -0.62 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 630 HIS 0.005 0.001 HIS B 951 PHE 0.018 0.002 PHE B 895 TYR 0.023 0.002 TYR B 393 ARG 0.009 0.000 ARG B 992 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 30) link_NAG-ASN : angle 2.64540 ( 90) hydrogen bonds : bond 0.05024 ( 1325) hydrogen bonds : angle 5.71724 ( 3582) SS BOND : bond 0.00289 ( 51) SS BOND : angle 0.84855 ( 102) covalent geometry : bond 0.00377 (31140) covalent geometry : angle 0.57162 (42369) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36165.99 seconds wall clock time: 631 minutes 49.28 seconds (37909.28 seconds total)