Starting phenix.real_space_refine on Tue May 27 18:57:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r1c_18807/05_2025/8r1c_18807.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r1c_18807/05_2025/8r1c_18807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r1c_18807/05_2025/8r1c_18807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r1c_18807/05_2025/8r1c_18807.map" model { file = "/net/cci-nas-00/data/ceres_data/8r1c_18807/05_2025/8r1c_18807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r1c_18807/05_2025/8r1c_18807.cif" } resolution = 2.2 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= 0.007 sd= 0.081 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 141 5.16 5 C 19377 2.51 5 N 5010 2.21 5 O 5898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.35s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30426 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8276 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 51, 'TRANS': 1004} Chain breaks: 6 Chain: "H" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 931 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 795 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 931 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 795 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "F" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 931 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "G" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 795 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "B" Number of atoms: 8276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8276 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 51, 'TRANS': 1004} Chain breaks: 6 Chain: "C" Number of atoms: 8276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8276 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 51, 'TRANS': 1004} Chain breaks: 6 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 Time building chain proxies: 16.59, per 1000 atoms: 0.55 Number of scatterers: 30426 At special positions: 0 Unit cell: (159.936, 152.633, 171.62, 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 141 16.00 O 5898 8.00 N 5010 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 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=2.04 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.04 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 H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 103 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS D 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 103 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.04 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=2.04 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 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 654 " " NAG A1302 " - " ASN A 714 " " NAG A1303 " - " ASN A 798 " " NAG A1304 " - " ASN A1131 " " NAG A1305 " - " ASN A 706 " " NAG A1306 " - " ASN A 613 " " NAG A1307 " - " ASN A1095 " " NAG A1308 " - " ASN A 279 " " NAG A1309 " - " ASN A1071 " " NAG A1310 " - " ASN A 231 " " NAG B1301 " - " ASN B 654 " " NAG B1302 " - " ASN B 714 " " NAG B1303 " - " ASN B 798 " " NAG B1304 " - " ASN B1131 " " NAG B1305 " - " ASN B 706 " " NAG B1306 " - " ASN B 613 " " NAG B1307 " - " ASN B1095 " " NAG B1308 " - " ASN B 279 " " NAG B1309 " - " ASN B1071 " " NAG B1310 " - " ASN B 231 " " NAG C1301 " - " ASN C 654 " " NAG C1302 " - " ASN C 714 " " NAG C1303 " - " ASN C 798 " " NAG C1304 " - " ASN C1131 " " NAG C1305 " - " ASN C 706 " " NAG C1306 " - " ASN C 613 " " NAG C1307 " - " ASN C1095 " " NAG C1308 " - " ASN C 279 " " NAG C1309 " - " ASN C1071 " " NAG C1310 " - " ASN C 231 " Time building additional restraints: 7.36 Conformation dependent library (CDL) restraints added in 3.8 seconds 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7194 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 69 sheets defined 22.9% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.90 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.750A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.759A pdb=" N VAL A 364 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 386 removed outlier: 4.526A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.669A 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 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: 3.649A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 845 through 853 removed outlier: 3.893A 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: 3.820A 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: 3.951A 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 Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.033A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 63 through 66 removed outlier: 3.505A pdb=" N LYS D 66 " --> pdb=" O PRO D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 66' Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 63 through 66 removed outlier: 3.509A pdb=" N LYS F 66 " --> pdb=" O PRO F 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 63 through 66' Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.750A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 removed outlier: 3.759A pdb=" N VAL B 364 " --> pdb=" O ASP B 361 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR B 366 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 386 removed outlier: 4.526A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.669A 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 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 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.649A 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: 3.893A 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: 3.820A 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: 3.952A 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 Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 4.034A 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 334 through 340 removed outlier: 3.750A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 368 removed outlier: 3.759A pdb=" N VAL C 364 " --> pdb=" O ASP C 361 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR C 366 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 386 removed outlier: 4.526A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.669A 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 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: 3.650A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 845 through 853 removed outlier: 3.893A 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: 3.820A 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: 3.952A 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 Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 4.033A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 27 removed outlier: 7.666A pdb=" N ASN A 58 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR A 266 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER A 202 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 52 removed outlier: 3.866A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 132 removed outlier: 5.949A pdb=" N GLU A 129 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA A 160 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN A 131 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 140 removed outlier: 3.990A pdb=" N ASP A 139 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 316 removed outlier: 4.397A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.204A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.567A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.145A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 701 removed outlier: 6.460A pdb=" N ASN A 700 " --> pdb=" O LYS B 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.857A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 725 removed outlier: 5.904A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.464A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB9, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.231A pdb=" N TRP H 36 " --> pdb=" O ARG H 52 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.988A pdb=" N ILE H 113 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP H 101 " --> pdb=" O PHE H 111 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N PHE H 111 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.411A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 9 through 12 removed outlier: 5.877A pdb=" N THR L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AC7, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.595A pdb=" N GLY D 51 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG D 40 " --> pdb=" O TRP D 49 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TRP D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.996A pdb=" N ILE D 113 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP D 101 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N PHE D 111 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.416A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 9 through 12 removed outlier: 5.914A pdb=" N THR E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AD4, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AD5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.597A pdb=" N GLY F 51 " --> pdb=" O TRP F 38 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG F 40 " --> pdb=" O TRP F 49 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP F 49 " --> pdb=" O ARG F 40 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.001A pdb=" N ILE F 113 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP F 101 " --> pdb=" O PHE F 111 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE F 111 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.436A pdb=" N TRP G 37 " --> pdb=" O MET G 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 9 through 12 removed outlier: 5.894A pdb=" N THR G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AE1, first strand: chain 'B' and resid 23 through 27 removed outlier: 7.666A pdb=" N ASN B 58 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR B 266 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER B 202 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 44 through 52 removed outlier: 3.866A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AE4, first strand: chain 'B' and resid 129 through 132 removed outlier: 5.950A pdb=" N GLU B 129 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA B 160 " --> pdb=" O GLU B 129 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN B 131 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 139 through 140 removed outlier: 3.990A pdb=" N ASP B 139 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 308 through 316 removed outlier: 4.397A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.203A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AE9, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.567A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AF2, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AF3, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.145A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 699 through 701 removed outlier: 6.460A pdb=" N ASN B 700 " --> pdb=" O LYS C 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.856A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 715 through 725 removed outlier: 5.903A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.464A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 1117 through 1119 Processing sheet with id=AF9, first strand: chain 'C' and resid 23 through 27 removed outlier: 7.666A pdb=" N ASN C 58 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR C 266 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 44 through 52 removed outlier: 3.866A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AG3, first strand: chain 'C' and resid 129 through 132 removed outlier: 5.948A pdb=" N GLU C 129 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA C 160 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN C 131 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 139 through 140 removed outlier: 3.990A pdb=" N ASP C 139 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 308 through 316 removed outlier: 4.397A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 321 through 325 removed outlier: 4.204A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AG8, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.567A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AH1, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AH2, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.145A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 708 through 712 removed outlier: 3.857A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 715 through 725 removed outlier: 5.904A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.464A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 1117 through 1119 1322 hydrogen bonds defined for protein. 3486 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: 14.52 Time building geometry restraints manager: 8.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.76 - 1.01: 2 1.01 - 1.26: 4921 1.26 - 1.50: 13997 1.50 - 1.75: 12030 1.75 - 2.00: 175 Bond restraints: 31125 Sorted by residual: bond pdb=" CG PRO F 9 " pdb=" CD PRO F 9 " ideal model delta sigma weight residual 1.503 0.759 0.744 3.40e-02 8.65e+02 4.78e+02 bond pdb=" CG PRO D 9 " pdb=" CD PRO D 9 " ideal model delta sigma weight residual 1.503 0.894 0.609 3.40e-02 8.65e+02 3.21e+02 bond pdb=" CB PRO F 9 " pdb=" CG PRO F 9 " ideal model delta sigma weight residual 1.492 2.001 -0.509 5.00e-02 4.00e+02 1.04e+02 bond pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 1.468 1.564 -0.096 1.20e-02 6.94e+03 6.44e+01 bond pdb=" CB PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 1.492 1.105 0.387 5.00e-02 4.00e+02 6.00e+01 ... (remaining 31120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 42348 14.77 - 29.55: 1 29.55 - 44.32: 6 44.32 - 59.09: 1 59.09 - 73.87: 1 Bond angle restraints: 42357 Sorted by residual: angle pdb=" N PRO D 9 " pdb=" CD PRO D 9 " pdb=" CG PRO D 9 " ideal model delta sigma weight residual 103.20 51.20 52.00 1.50e+00 4.44e-01 1.20e+03 angle pdb=" N PRO F 9 " pdb=" CD PRO F 9 " pdb=" CG PRO F 9 " ideal model delta sigma weight residual 103.20 62.65 40.55 1.50e+00 4.44e-01 7.31e+02 angle pdb=" N PRO H 9 " pdb=" CD PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 103.20 67.36 35.84 1.50e+00 4.44e-01 5.71e+02 angle pdb=" CB PRO H 9 " pdb=" CG PRO H 9 " pdb=" CD PRO H 9 " ideal model delta sigma weight residual 106.10 179.97 -73.87 3.20e+00 9.77e-02 5.33e+02 angle pdb=" CA PRO D 9 " pdb=" CB PRO D 9 " pdb=" CG PRO D 9 " ideal model delta sigma weight residual 104.50 61.12 43.38 1.90e+00 2.77e-01 5.21e+02 ... (remaining 42352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.75: 17724 22.75 - 45.50: 896 45.50 - 68.25: 160 68.25 - 91.00: 70 91.00 - 113.75: 2 Dihedral angle restraints: 18852 sinusoidal: 7632 harmonic: 11220 Sorted by residual: dihedral pdb=" N PRO F 9 " pdb=" C PRO F 9 " pdb=" CA PRO F 9 " pdb=" CB PRO F 9 " ideal model delta harmonic sigma weight residual 115.10 97.53 17.57 0 2.50e+00 1.60e-01 4.94e+01 dihedral pdb=" CA PRO D 9 " pdb=" CB PRO D 9 " pdb=" CG PRO D 9 " pdb=" CD PRO D 9 " ideal model delta sinusoidal sigma weight residual 38.00 151.75 -113.75 1 2.00e+01 2.50e-03 3.37e+01 dihedral pdb=" N PRO D 9 " pdb=" CG PRO D 9 " pdb=" CD PRO D 9 " pdb=" CB PRO D 9 " ideal model delta sinusoidal sigma weight residual 30.00 107.23 -77.23 1 1.50e+01 4.44e-03 3.32e+01 ... (remaining 18849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3625 0.048 - 0.096: 974 0.096 - 0.144: 276 0.144 - 0.192: 10 0.192 - 0.240: 2 Chirality restraints: 4887 Sorted by residual: chirality pdb=" CA PRO H 9 " pdb=" N PRO H 9 " pdb=" C PRO H 9 " pdb=" CB PRO H 9 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA PRO D 9 " pdb=" N PRO D 9 " pdb=" C PRO D 9 " pdb=" CB PRO D 9 " both_signs ideal model delta sigma weight residual False 2.72 2.95 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA PRO F 9 " pdb=" N PRO F 9 " pdb=" C PRO F 9 " pdb=" CB PRO F 9 " both_signs ideal model delta sigma weight residual False 2.72 2.89 -0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 4884 not shown) Planarity restraints: 5436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 8 " -0.106 5.00e-02 4.00e+02 1.52e-01 3.68e+01 pdb=" N PRO H 9 " 0.262 5.00e-02 4.00e+02 pdb=" CA PRO H 9 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO H 9 " -0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 8 " 0.086 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO D 9 " -0.212 5.00e-02 4.00e+02 pdb=" CA PRO D 9 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO D 9 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS L 41 " 0.072 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO L 42 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO L 42 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 42 " 0.057 5.00e-02 4.00e+02 ... (remaining 5433 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 255 2.65 - 3.22: 26987 3.22 - 3.78: 46994 3.78 - 4.34: 69218 4.34 - 4.90: 110180 Nonbonded interactions: 253634 Sorted by model distance: nonbonded pdb=" OG1 THR C 596 " pdb=" O PRO C 597 " model vdw 2.093 3.040 nonbonded pdb=" OG1 THR A 596 " pdb=" O PRO A 597 " model vdw 2.093 3.040 nonbonded pdb=" OG1 THR B 596 " pdb=" O PRO B 597 " model vdw 2.094 3.040 nonbonded pdb=" O THR B 390 " pdb=" OG1 THR B 520 " model vdw 2.112 3.040 nonbonded pdb=" O THR C 390 " pdb=" OG1 THR C 520 " model vdw 2.112 3.040 ... (remaining 253629 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: 0.13 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.440 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 67.570 Find NCS groups from input model: 1.060 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: 0.010 Load rotamer database and sin/cos tables:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 0.744 31206 Z= 0.274 Angle : 0.879 73.867 42549 Z= 0.473 Chirality : 0.046 0.240 4887 Planarity : 0.005 0.152 5406 Dihedral : 14.579 113.749 11505 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.07 % Allowed : 10.53 % Favored : 88.39 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 3813 helix: 1.93 (0.20), residues: 714 sheet: 0.29 (0.15), residues: 1023 loop : -0.61 (0.12), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.007 0.001 HIS A 516 PHE 0.015 0.001 PHE B 895 TYR 0.018 0.001 TYR C1064 ARG 0.002 0.000 ARG C1016 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 30) link_NAG-ASN : angle 3.07928 ( 90) hydrogen bonds : bond 0.10424 ( 1292) hydrogen bonds : angle 6.39598 ( 3486) SS BOND : bond 0.00223 ( 51) SS BOND : angle 0.65487 ( 102) covalent geometry : bond 0.00783 (31125) covalent geometry : angle 0.86934 (42357) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 3.156 Fit side-chains REVERT: H 40 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7339 (ptt180) REVERT: F 9 PRO cc_start: 0.6117 (OUTLIER) cc_final: 0.5888 (Cg_exo) REVERT: F 101 ASP cc_start: 0.8005 (t0) cc_final: 0.7804 (t0) REVERT: F 119 MET cc_start: 0.6791 (mtt) cc_final: 0.6381 (mpp) REVERT: B 118 ASN cc_start: 0.7095 (t0) cc_final: 0.6701 (m110) REVERT: B 150 MET cc_start: 0.6046 (tmm) cc_final: 0.5601 (pp-130) REVERT: B 776 GLN cc_start: 0.8858 (tt0) cc_final: 0.8581 (tp40) REVERT: B 897 MET cc_start: 0.9325 (mtp) cc_final: 0.9092 (mtp) REVERT: B 932 GLN cc_start: 0.7847 (tt0) cc_final: 0.7640 (tt0) REVERT: B 1070 LYS cc_start: 0.8608 (mttt) cc_final: 0.8290 (mtpp) REVERT: C 150 MET cc_start: 0.6036 (tmm) cc_final: 0.5403 (pp-130) REVERT: C 742 ASP cc_start: 0.8132 (p0) cc_final: 0.7931 (p0) REVERT: C 776 GLN cc_start: 0.8888 (tt0) cc_final: 0.8672 (tp40) REVERT: C 1070 LYS cc_start: 0.8632 (mttt) cc_final: 0.8244 (mtpp) outliers start: 36 outliers final: 23 residues processed: 273 average time/residue: 1.3251 time to fit residues: 433.1646 Evaluate side-chains 249 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 9 PRO Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 782 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 10.0000 chunk 288 optimal weight: 20.0000 chunk 160 optimal weight: 30.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 298 optimal weight: 20.0000 chunk 115 optimal weight: 30.0000 chunk 181 optimal weight: 40.0000 chunk 222 optimal weight: 8.9990 chunk 345 optimal weight: 9.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 999 GLN H 116 GLN B 447 ASN B 561 GLN B 910 GLN B 999 GLN C 23 GLN C 118 ASN C 561 GLN C 610 GLN C 910 GLN C 999 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.187325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.114078 restraints weight = 27810.266| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.14 r_work: 0.3047 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.0553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 31206 Z= 0.185 Angle : 0.599 14.835 42549 Z= 0.317 Chirality : 0.047 0.188 4887 Planarity : 0.004 0.046 5406 Dihedral : 5.514 43.188 4806 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.88 % Allowed : 10.03 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.13), residues: 3813 helix: 2.12 (0.20), residues: 693 sheet: 0.33 (0.15), residues: 1005 loop : -0.56 (0.12), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 36 HIS 0.008 0.001 HIS C 516 PHE 0.020 0.002 PHE B 895 TYR 0.019 0.002 TYR A1064 ARG 0.006 0.001 ARG B 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 30) link_NAG-ASN : angle 3.22910 ( 90) hydrogen bonds : bond 0.05577 ( 1292) hydrogen bonds : angle 5.79690 ( 3486) SS BOND : bond 0.00291 ( 51) SS BOND : angle 0.75773 ( 102) covalent geometry : bond 0.00422 (31125) covalent geometry : angle 0.58038 (42357) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 236 time to evaluate : 3.160 Fit side-chains REVERT: A 455 LYS cc_start: 0.8459 (mmtt) cc_final: 0.7886 (mtmm) REVERT: A 643 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8072 (mtp180) REVERT: L 87 ASP cc_start: 0.6938 (OUTLIER) cc_final: 0.6517 (t0) REVERT: D 40 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6605 (ptt180) REVERT: E 40 GLN cc_start: 0.6425 (OUTLIER) cc_final: 0.5667 (tt0) REVERT: E 87 ASP cc_start: 0.6658 (OUTLIER) cc_final: 0.5974 (m-30) REVERT: F 119 MET cc_start: 0.7113 (mtt) cc_final: 0.6185 (mpp) REVERT: B 118 ASN cc_start: 0.6915 (t0) cc_final: 0.6545 (m110) REVERT: B 150 MET cc_start: 0.5990 (OUTLIER) cc_final: 0.5290 (pp-130) REVERT: B 332 LEU cc_start: 0.8042 (mm) cc_final: 0.7747 (mm) REVERT: B 455 LYS cc_start: 0.8387 (mmtt) cc_final: 0.7810 (mtmt) REVERT: B 643 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7212 (mpp-170) REVERT: B 776 GLN cc_start: 0.8977 (tt0) cc_final: 0.8453 (tp40) REVERT: B 932 GLN cc_start: 0.7890 (tt0) cc_final: 0.7629 (tt0) REVERT: B 1070 LYS cc_start: 0.8768 (mttt) cc_final: 0.8169 (mptt) REVERT: C 150 MET cc_start: 0.6243 (OUTLIER) cc_final: 0.5311 (pp-130) REVERT: C 643 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7632 (mtp180) REVERT: C 742 ASP cc_start: 0.8237 (p0) cc_final: 0.8012 (p0) REVERT: C 1070 LYS cc_start: 0.8758 (mttt) cc_final: 0.8332 (mtpp) outliers start: 63 outliers final: 21 residues processed: 281 average time/residue: 1.2858 time to fit residues: 432.9173 Evaluate side-chains 263 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 110 optimal weight: 2.9990 chunk 259 optimal weight: 8.9990 chunk 166 optimal weight: 20.0000 chunk 131 optimal weight: 0.6980 chunk 234 optimal weight: 3.9990 chunk 358 optimal weight: 6.9990 chunk 117 optimal weight: 0.0050 chunk 273 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 overall best weight: 2.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN A 999 GLN H 116 GLN B 447 ASN B 561 GLN B 999 GLN C 118 ASN C 561 GLN C 999 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.188783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117234 restraints weight = 28083.794| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.01 r_work: 0.3108 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31206 Z= 0.118 Angle : 0.512 10.564 42549 Z= 0.270 Chirality : 0.044 0.162 4887 Planarity : 0.003 0.036 5406 Dihedral : 4.954 44.707 4780 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.43 % Allowed : 10.36 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.42 (0.13), residues: 3813 helix: 2.46 (0.20), residues: 675 sheet: 0.42 (0.16), residues: 987 loop : -0.49 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.005 0.001 HIS A 516 PHE 0.014 0.001 PHE B 895 TYR 0.017 0.001 TYR B1064 ARG 0.005 0.000 ARG B 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 30) link_NAG-ASN : angle 3.01252 ( 90) hydrogen bonds : bond 0.04661 ( 1292) hydrogen bonds : angle 5.50408 ( 3486) SS BOND : bond 0.00181 ( 51) SS BOND : angle 0.56862 ( 102) covalent geometry : bond 0.00255 (31125) covalent geometry : angle 0.49321 (42357) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 3.415 Fit side-chains REVERT: A 138 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6810 (mp) REVERT: A 169 SER cc_start: 0.7126 (OUTLIER) cc_final: 0.6854 (m) REVERT: A 228 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6933 (pp) REVERT: A 455 LYS cc_start: 0.8500 (mmtt) cc_final: 0.7897 (mtmm) REVERT: A 643 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7714 (mtp180) REVERT: D 40 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6676 (ptt180) REVERT: E 40 GLN cc_start: 0.6378 (OUTLIER) cc_final: 0.5474 (tt0) REVERT: E 87 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.6157 (m-30) REVERT: F 119 MET cc_start: 0.7137 (mtt) cc_final: 0.6201 (mpp) REVERT: B 118 ASN cc_start: 0.6986 (t0) cc_final: 0.6575 (m110) REVERT: B 150 MET cc_start: 0.6388 (tmm) cc_final: 0.5609 (pp-130) REVERT: B 455 LYS cc_start: 0.8458 (mmtt) cc_final: 0.7848 (mtmt) REVERT: B 643 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7214 (mpp-170) REVERT: B 776 GLN cc_start: 0.8950 (tt0) cc_final: 0.8486 (tp40) REVERT: B 805 ASP cc_start: 0.7334 (t0) cc_final: 0.7099 (t0) REVERT: B 932 GLN cc_start: 0.7903 (tt0) cc_final: 0.7662 (tt0) REVERT: B 1070 LYS cc_start: 0.8726 (mttt) cc_final: 0.8188 (mptt) REVERT: B 1098 HIS cc_start: 0.8761 (m90) cc_final: 0.8407 (m90) REVERT: C 150 MET cc_start: 0.6310 (tmm) cc_final: 0.5381 (pp-130) REVERT: C 169 SER cc_start: 0.7101 (OUTLIER) cc_final: 0.6883 (m) REVERT: C 332 LEU cc_start: 0.7989 (mm) cc_final: 0.7753 (mm) REVERT: C 643 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7613 (mtp180) REVERT: C 742 ASP cc_start: 0.8248 (p0) cc_final: 0.7997 (p0) REVERT: C 1070 LYS cc_start: 0.8712 (mttt) cc_final: 0.8324 (mtpp) outliers start: 48 outliers final: 14 residues processed: 281 average time/residue: 1.3148 time to fit residues: 442.3252 Evaluate side-chains 255 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 3.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 643 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 115 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 297 optimal weight: 7.9990 chunk 288 optimal weight: 40.0000 chunk 48 optimal weight: 10.0000 chunk 127 optimal weight: 40.0000 chunk 62 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN H 116 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN B 561 GLN B 999 GLN C 118 ASN C 561 GLN C 999 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.186310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114465 restraints weight = 27978.476| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.21 r_work: 0.3037 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 31206 Z= 0.252 Angle : 0.639 10.906 42549 Z= 0.341 Chirality : 0.050 0.224 4887 Planarity : 0.005 0.060 5406 Dihedral : 5.585 47.793 4779 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.00 % Allowed : 10.15 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.13), residues: 3813 helix: 1.92 (0.20), residues: 696 sheet: 0.22 (0.15), residues: 1014 loop : -0.57 (0.12), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 36 HIS 0.009 0.002 HIS C 516 PHE 0.023 0.002 PHE B 895 TYR 0.023 0.002 TYR C 753 ARG 0.007 0.001 ARG B 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 30) link_NAG-ASN : angle 3.25906 ( 90) hydrogen bonds : bond 0.06116 ( 1292) hydrogen bonds : angle 5.88611 ( 3486) SS BOND : bond 0.00402 ( 51) SS BOND : angle 0.92448 ( 102) covalent geometry : bond 0.00581 (31125) covalent geometry : angle 0.62060 (42357) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 233 time to evaluate : 3.136 Fit side-chains REVERT: A 455 LYS cc_start: 0.8492 (mmtt) cc_final: 0.7905 (mtmm) REVERT: A 643 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8074 (mtp180) REVERT: A 961 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8343 (mtpt) REVERT: A 983 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7376 (ttpt) REVERT: D 40 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6678 (ptt180) REVERT: E 40 GLN cc_start: 0.6470 (OUTLIER) cc_final: 0.5539 (tt0) REVERT: E 87 ASP cc_start: 0.6761 (OUTLIER) cc_final: 0.6097 (m-30) REVERT: B 118 ASN cc_start: 0.7060 (t0) cc_final: 0.6719 (m110) REVERT: B 150 MET cc_start: 0.6084 (OUTLIER) cc_final: 0.5699 (mpt) REVERT: B 332 LEU cc_start: 0.8088 (mm) cc_final: 0.7794 (mm) REVERT: B 437 LYS cc_start: 0.8251 (mttt) cc_final: 0.8015 (mtpt) REVERT: B 643 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7242 (mpp-170) REVERT: B 776 GLN cc_start: 0.9059 (tt0) cc_final: 0.8581 (tp40) REVERT: B 847 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7685 (mp) REVERT: B 932 GLN cc_start: 0.8009 (tt0) cc_final: 0.7754 (tt0) REVERT: B 961 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8074 (mppt) REVERT: B 1070 LYS cc_start: 0.8837 (mttt) cc_final: 0.8294 (mptt) REVERT: C 118 ASN cc_start: 0.7139 (OUTLIER) cc_final: 0.6666 (m110) REVERT: C 138 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6841 (mp) REVERT: C 150 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5202 (pp-130) REVERT: C 332 LEU cc_start: 0.7944 (mm) cc_final: 0.7671 (mm) REVERT: C 643 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7904 (mtp180) REVERT: C 742 ASP cc_start: 0.8259 (p0) cc_final: 0.8032 (p0) REVERT: C 1070 LYS cc_start: 0.8814 (mttt) cc_final: 0.8445 (mtpp) outliers start: 67 outliers final: 30 residues processed: 282 average time/residue: 1.3288 time to fit residues: 447.2355 Evaluate side-chains 275 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 961 LYS Chi-restraints excluded: chain A residue 983 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 90 optimal weight: 2.9990 chunk 147 optimal weight: 40.0000 chunk 134 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 264 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 341 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 373 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN A 999 GLN H 116 GLN B 561 GLN B 999 GLN C 561 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.188025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117592 restraints weight = 27991.581| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.15 r_work: 0.3075 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31206 Z= 0.134 Angle : 0.535 10.524 42549 Z= 0.282 Chirality : 0.045 0.167 4887 Planarity : 0.004 0.036 5406 Dihedral : 5.177 47.700 4779 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.31 % Allowed : 11.10 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.13), residues: 3813 helix: 2.32 (0.20), residues: 675 sheet: 0.34 (0.16), residues: 978 loop : -0.52 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.006 0.001 HIS A 516 PHE 0.015 0.001 PHE B 895 TYR 0.018 0.001 TYR A1064 ARG 0.006 0.000 ARG B 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 30) link_NAG-ASN : angle 3.06219 ( 90) hydrogen bonds : bond 0.04934 ( 1292) hydrogen bonds : angle 5.59662 ( 3486) SS BOND : bond 0.00206 ( 51) SS BOND : angle 0.63185 ( 102) covalent geometry : bond 0.00293 (31125) covalent geometry : angle 0.51603 (42357) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 3.098 Fit side-chains REVERT: A 455 LYS cc_start: 0.8508 (mmtt) cc_final: 0.7884 (mtmm) REVERT: A 643 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7738 (mtp180) REVERT: D 40 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6678 (ptt180) REVERT: E 40 GLN cc_start: 0.6347 (OUTLIER) cc_final: 0.5410 (tt0) REVERT: E 87 ASP cc_start: 0.6752 (OUTLIER) cc_final: 0.6104 (m-30) REVERT: B 118 ASN cc_start: 0.6974 (t0) cc_final: 0.6633 (m110) REVERT: B 150 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5749 (mpt) REVERT: B 332 LEU cc_start: 0.8071 (mm) cc_final: 0.7806 (mm) REVERT: B 437 LYS cc_start: 0.8225 (mttt) cc_final: 0.7967 (mtpt) REVERT: B 643 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7256 (mpp-170) REVERT: B 776 GLN cc_start: 0.9040 (tt0) cc_final: 0.8560 (tp40) REVERT: B 805 ASP cc_start: 0.7474 (t0) cc_final: 0.7195 (t0) REVERT: B 847 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7702 (mp) REVERT: B 932 GLN cc_start: 0.7982 (tt0) cc_final: 0.7712 (tt0) REVERT: B 1070 LYS cc_start: 0.8816 (mttt) cc_final: 0.8291 (mptt) REVERT: C 118 ASN cc_start: 0.7031 (t0) cc_final: 0.6655 (m110) REVERT: C 138 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6755 (mp) REVERT: C 150 MET cc_start: 0.6222 (OUTLIER) cc_final: 0.5279 (pp-130) REVERT: C 318 GLN cc_start: 0.8369 (mm110) cc_final: 0.8168 (mm110) REVERT: C 332 LEU cc_start: 0.7948 (mm) cc_final: 0.7616 (mm) REVERT: C 437 LYS cc_start: 0.8226 (mttt) cc_final: 0.7999 (mtpt) REVERT: C 643 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7664 (mtp180) REVERT: C 742 ASP cc_start: 0.8260 (p0) cc_final: 0.8010 (p0) REVERT: C 1070 LYS cc_start: 0.8796 (mttt) cc_final: 0.8417 (mtpp) outliers start: 44 outliers final: 17 residues processed: 271 average time/residue: 1.3616 time to fit residues: 438.7464 Evaluate side-chains 259 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 324 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 168 optimal weight: 50.0000 chunk 126 optimal weight: 20.0000 chunk 290 optimal weight: 9.9990 chunk 243 optimal weight: 0.9990 chunk 317 optimal weight: 9.9990 chunk 354 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 113 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 561 GLN A 999 GLN H 116 GLN B 561 GLN B 999 GLN C 122 ASN C 561 GLN C 999 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.186644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114698 restraints weight = 27814.979| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.15 r_work: 0.3041 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 31206 Z= 0.209 Angle : 0.604 10.612 42549 Z= 0.320 Chirality : 0.048 0.196 4887 Planarity : 0.004 0.050 5406 Dihedral : 5.487 49.192 4779 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.55 % Allowed : 11.43 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.13), residues: 3813 helix: 2.11 (0.20), residues: 675 sheet: 0.21 (0.15), residues: 1014 loop : -0.60 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 36 HIS 0.007 0.001 HIS C 516 PHE 0.021 0.002 PHE B 895 TYR 0.021 0.002 TYR A 753 ARG 0.006 0.001 ARG B 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 30) link_NAG-ASN : angle 3.16613 ( 90) hydrogen bonds : bond 0.05763 ( 1292) hydrogen bonds : angle 5.79962 ( 3486) SS BOND : bond 0.00336 ( 51) SS BOND : angle 0.81825 ( 102) covalent geometry : bond 0.00477 (31125) covalent geometry : angle 0.58589 (42357) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 228 time to evaluate : 3.541 Fit side-chains REVERT: A 437 LYS cc_start: 0.8331 (mttt) cc_final: 0.8052 (mtpt) REVERT: A 455 LYS cc_start: 0.8532 (mmtt) cc_final: 0.7924 (mtmm) REVERT: A 643 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8056 (mtp180) REVERT: A 792 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.6102 (tmtt) REVERT: A 961 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8138 (mppt) REVERT: A 983 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7361 (ttpt) REVERT: L 40 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.4560 (tp40) REVERT: D 40 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6696 (ptt180) REVERT: E 40 GLN cc_start: 0.6427 (OUTLIER) cc_final: 0.5408 (tt0) REVERT: E 87 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.6057 (m-30) REVERT: B 118 ASN cc_start: 0.7015 (t0) cc_final: 0.6704 (m110) REVERT: B 150 MET cc_start: 0.6003 (OUTLIER) cc_final: 0.5580 (mpt) REVERT: B 332 LEU cc_start: 0.8106 (mm) cc_final: 0.7826 (mm) REVERT: B 437 LYS cc_start: 0.8228 (mttt) cc_final: 0.7968 (mtpt) REVERT: B 643 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7243 (mpp-170) REVERT: B 776 GLN cc_start: 0.9039 (tt0) cc_final: 0.8568 (tp40) REVERT: B 847 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7683 (mp) REVERT: B 932 GLN cc_start: 0.8012 (tt0) cc_final: 0.7737 (tt0) REVERT: B 961 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8070 (mppt) REVERT: B 1070 LYS cc_start: 0.8838 (mttt) cc_final: 0.8311 (mptt) REVERT: C 138 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6781 (mp) REVERT: C 150 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.5354 (pp-130) REVERT: C 332 LEU cc_start: 0.7953 (mm) cc_final: 0.7623 (mm) REVERT: C 437 LYS cc_start: 0.8268 (mttt) cc_final: 0.8035 (mtpt) REVERT: C 643 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7705 (mtp180) REVERT: C 742 ASP cc_start: 0.8247 (p0) cc_final: 0.8008 (p0) REVERT: C 1070 LYS cc_start: 0.8805 (mttt) cc_final: 0.8438 (mtpp) outliers start: 52 outliers final: 23 residues processed: 265 average time/residue: 1.3896 time to fit residues: 437.8026 Evaluate side-chains 264 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LYS Chi-restraints excluded: chain A residue 961 LYS Chi-restraints excluded: chain A residue 983 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 274 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 360 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 340 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 143 optimal weight: 0.9990 chunk 328 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 306 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN A 999 GLN H 116 GLN B 561 GLN B 999 GLN C 561 GLN C 625 GLN C 999 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.187313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112866 restraints weight = 27864.219| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.01 r_work: 0.3084 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31206 Z= 0.161 Angle : 0.559 10.477 42549 Z= 0.295 Chirality : 0.046 0.171 4887 Planarity : 0.004 0.040 5406 Dihedral : 5.288 49.408 4779 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.79 % Allowed : 11.22 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.13), residues: 3813 helix: 2.11 (0.20), residues: 693 sheet: 0.35 (0.15), residues: 975 loop : -0.54 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 36 HIS 0.006 0.001 HIS A 516 PHE 0.017 0.001 PHE B 895 TYR 0.019 0.001 TYR A1064 ARG 0.006 0.000 ARG B 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 30) link_NAG-ASN : angle 3.07021 ( 90) hydrogen bonds : bond 0.05216 ( 1292) hydrogen bonds : angle 5.65702 ( 3486) SS BOND : bond 0.00249 ( 51) SS BOND : angle 0.69864 ( 102) covalent geometry : bond 0.00359 (31125) covalent geometry : angle 0.54108 (42357) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 229 time to evaluate : 3.101 Fit side-chains REVERT: A 316 ARG cc_start: 0.7465 (mtt-85) cc_final: 0.7148 (mpt90) REVERT: A 437 LYS cc_start: 0.8244 (mttt) cc_final: 0.7960 (mtpt) REVERT: A 455 LYS cc_start: 0.8483 (mmtt) cc_final: 0.7874 (mtmm) REVERT: A 643 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7593 (mtp180) REVERT: A 792 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.5926 (tmtt) REVERT: L 28 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7508 (p0) REVERT: L 40 GLN cc_start: 0.6464 (OUTLIER) cc_final: 0.4473 (tp40) REVERT: D 40 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6577 (ptt180) REVERT: E 40 GLN cc_start: 0.6189 (OUTLIER) cc_final: 0.5212 (tt0) REVERT: E 87 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.6024 (m-30) REVERT: B 118 ASN cc_start: 0.6880 (t0) cc_final: 0.6565 (m110) REVERT: B 150 MET cc_start: 0.5971 (OUTLIER) cc_final: 0.5565 (mpt) REVERT: B 318 GLN cc_start: 0.8118 (mm110) cc_final: 0.7910 (mm110) REVERT: B 437 LYS cc_start: 0.8142 (mttt) cc_final: 0.7861 (mtpt) REVERT: B 643 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7077 (mpp-170) REVERT: B 776 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8376 (tp40) REVERT: B 847 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7569 (mp) REVERT: B 932 GLN cc_start: 0.7923 (tt0) cc_final: 0.7617 (tt0) REVERT: B 961 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7859 (mppt) REVERT: B 1070 LYS cc_start: 0.8718 (mttt) cc_final: 0.8117 (mptt) REVERT: C 138 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6789 (mp) REVERT: C 150 MET cc_start: 0.6211 (OUTLIER) cc_final: 0.5289 (pp-130) REVERT: C 169 SER cc_start: 0.7115 (OUTLIER) cc_final: 0.6905 (m) REVERT: C 332 LEU cc_start: 0.7859 (mm) cc_final: 0.7514 (mm) REVERT: C 437 LYS cc_start: 0.8186 (mttt) cc_final: 0.7924 (mtpt) REVERT: C 643 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7537 (mtp180) REVERT: C 742 ASP cc_start: 0.8153 (p0) cc_final: 0.7902 (p0) REVERT: C 1070 LYS cc_start: 0.8689 (mttt) cc_final: 0.8261 (mtpp) outliers start: 60 outliers final: 26 residues processed: 272 average time/residue: 1.3445 time to fit residues: 434.6994 Evaluate side-chains 264 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 776 GLN Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 170 optimal weight: 30.0000 chunk 183 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 354 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 121 optimal weight: 40.0000 chunk 306 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 71 optimal weight: 0.0050 chunk 258 optimal weight: 10.0000 chunk 301 optimal weight: 2.9990 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN A 999 GLN H 116 GLN B 561 GLN B 999 GLN C 561 GLN C 999 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.187503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115942 restraints weight = 27886.779| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.03 r_work: 0.3065 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31206 Z= 0.151 Angle : 0.553 10.401 42549 Z= 0.291 Chirality : 0.046 0.167 4887 Planarity : 0.004 0.038 5406 Dihedral : 5.215 49.775 4779 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.85 % Allowed : 11.31 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.13), residues: 3813 helix: 2.15 (0.20), residues: 693 sheet: 0.38 (0.16), residues: 975 loop : -0.52 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 36 HIS 0.006 0.001 HIS C 516 PHE 0.017 0.001 PHE B 895 TYR 0.018 0.001 TYR A1064 ARG 0.009 0.000 ARG B 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 30) link_NAG-ASN : angle 3.03546 ( 90) hydrogen bonds : bond 0.05113 ( 1292) hydrogen bonds : angle 5.61456 ( 3486) SS BOND : bond 0.00238 ( 51) SS BOND : angle 0.66105 ( 102) covalent geometry : bond 0.00336 (31125) covalent geometry : angle 0.53516 (42357) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 231 time to evaluate : 3.367 Fit side-chains REVERT: A 316 ARG cc_start: 0.7504 (mtt-85) cc_final: 0.7211 (mpt90) REVERT: A 437 LYS cc_start: 0.8280 (mttt) cc_final: 0.8000 (mtpt) REVERT: A 455 LYS cc_start: 0.8513 (mmtt) cc_final: 0.7903 (mtmm) REVERT: A 643 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7673 (mtp180) REVERT: A 792 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.5952 (tmtt) REVERT: L 28 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7646 (p0) REVERT: L 40 GLN cc_start: 0.6525 (OUTLIER) cc_final: 0.4527 (tp40) REVERT: D 40 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6619 (ptt180) REVERT: E 40 GLN cc_start: 0.6298 (OUTLIER) cc_final: 0.5249 (tt0) REVERT: E 87 ASP cc_start: 0.6680 (OUTLIER) cc_final: 0.6058 (m-30) REVERT: F 40 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6666 (ptt180) REVERT: B 118 ASN cc_start: 0.6940 (t0) cc_final: 0.6621 (m110) REVERT: B 150 MET cc_start: 0.6013 (OUTLIER) cc_final: 0.5617 (mpt) REVERT: B 332 LEU cc_start: 0.8035 (mm) cc_final: 0.7769 (mm) REVERT: B 437 LYS cc_start: 0.8178 (mttt) cc_final: 0.7901 (mtpt) REVERT: B 643 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7151 (mpp-170) REVERT: B 776 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8463 (tp40) REVERT: B 847 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7656 (mp) REVERT: B 932 GLN cc_start: 0.8003 (tt0) cc_final: 0.7708 (tt0) REVERT: B 961 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7937 (mppt) REVERT: B 1070 LYS cc_start: 0.8773 (mttt) cc_final: 0.8202 (mptt) REVERT: C 138 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6826 (mp) REVERT: C 150 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5266 (pp-130) REVERT: C 169 SER cc_start: 0.7197 (OUTLIER) cc_final: 0.6986 (m) REVERT: C 318 GLN cc_start: 0.8288 (mm110) cc_final: 0.8085 (mm110) REVERT: C 332 LEU cc_start: 0.7872 (mm) cc_final: 0.7518 (mm) REVERT: C 437 LYS cc_start: 0.8197 (mttt) cc_final: 0.7965 (mtpt) REVERT: C 643 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7599 (mtp180) REVERT: C 742 ASP cc_start: 0.8224 (p0) cc_final: 0.7965 (p0) REVERT: C 776 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: C 1070 LYS cc_start: 0.8757 (mttt) cc_final: 0.8344 (mtpp) outliers start: 62 outliers final: 30 residues processed: 277 average time/residue: 1.3824 time to fit residues: 456.9418 Evaluate side-chains 278 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 230 time to evaluate : 3.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 776 GLN Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 6 optimal weight: 30.0000 chunk 169 optimal weight: 40.0000 chunk 343 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 273 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 367 optimal weight: 2.9990 chunk 334 optimal weight: 0.9980 chunk 372 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 290 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN A 999 GLN H 116 GLN F 116 GLN B 561 GLN B 999 GLN C 561 GLN C 999 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.188657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114696 restraints weight = 27960.093| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.09 r_work: 0.3112 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 31206 Z= 0.115 Angle : 0.515 10.410 42549 Z= 0.269 Chirality : 0.044 0.157 4887 Planarity : 0.003 0.036 5406 Dihedral : 4.947 49.342 4779 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.58 % Allowed : 11.67 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.13), residues: 3813 helix: 2.32 (0.20), residues: 693 sheet: 0.44 (0.16), residues: 975 loop : -0.45 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 36 HIS 0.005 0.001 HIS A 516 PHE 0.014 0.001 PHE C 562 TYR 0.017 0.001 TYR A1064 ARG 0.010 0.000 ARG B 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 30) link_NAG-ASN : angle 2.93859 ( 90) hydrogen bonds : bond 0.04520 ( 1292) hydrogen bonds : angle 5.42328 ( 3486) SS BOND : bond 0.00167 ( 51) SS BOND : angle 0.56107 ( 102) covalent geometry : bond 0.00247 (31125) covalent geometry : angle 0.49699 (42357) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 243 time to evaluate : 3.180 Fit side-chains REVERT: A 316 ARG cc_start: 0.7422 (mtt-85) cc_final: 0.7148 (mpt90) REVERT: A 355 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7880 (mt) REVERT: A 437 LYS cc_start: 0.8201 (mttt) cc_final: 0.7928 (mtpt) REVERT: A 455 LYS cc_start: 0.8460 (mmtt) cc_final: 0.7821 (mtmm) REVERT: A 643 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7577 (mtp180) REVERT: A 792 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.6013 (tttm) REVERT: L 28 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7463 (p0) REVERT: L 40 GLN cc_start: 0.6405 (OUTLIER) cc_final: 0.4214 (tp40) REVERT: D 40 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6526 (ptt180) REVERT: E 40 GLN cc_start: 0.6102 (OUTLIER) cc_final: 0.5069 (tt0) REVERT: E 87 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6045 (m-30) REVERT: F 101 ASP cc_start: 0.7731 (t0) cc_final: 0.7519 (t0) REVERT: B 150 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.5838 (mpt) REVERT: B 318 GLN cc_start: 0.8123 (mm110) cc_final: 0.7873 (mm110) REVERT: B 332 LEU cc_start: 0.7997 (mm) cc_final: 0.7751 (mm) REVERT: B 437 LYS cc_start: 0.8194 (mttt) cc_final: 0.7903 (mtpt) REVERT: B 643 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7103 (mpp-170) REVERT: B 742 ASP cc_start: 0.8232 (p0) cc_final: 0.8029 (p0) REVERT: B 776 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8352 (tp40) REVERT: B 805 ASP cc_start: 0.7178 (t0) cc_final: 0.6859 (t0) REVERT: B 847 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7576 (mp) REVERT: B 932 GLN cc_start: 0.7916 (tt0) cc_final: 0.7621 (tt0) REVERT: B 1070 LYS cc_start: 0.8694 (mttt) cc_final: 0.8085 (mptt) REVERT: C 138 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6848 (mp) REVERT: C 150 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.5310 (pp-130) REVERT: C 169 SER cc_start: 0.7104 (OUTLIER) cc_final: 0.6901 (m) REVERT: C 318 GLN cc_start: 0.8209 (mm110) cc_final: 0.7996 (mm110) REVERT: C 332 LEU cc_start: 0.7804 (mm) cc_final: 0.7437 (mm) REVERT: C 437 LYS cc_start: 0.8138 (mttt) cc_final: 0.7901 (mtpt) REVERT: C 643 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7517 (mtp180) REVERT: C 742 ASP cc_start: 0.8147 (p0) cc_final: 0.7881 (p0) REVERT: C 776 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: C 1070 LYS cc_start: 0.8688 (mttt) cc_final: 0.8245 (mtpp) outliers start: 53 outliers final: 26 residues processed: 281 average time/residue: 1.3207 time to fit residues: 442.0719 Evaluate side-chains 272 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 3.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 792 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 776 GLN Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 361 optimal weight: 20.0000 chunk 218 optimal weight: 8.9990 chunk 304 optimal weight: 0.5980 chunk 194 optimal weight: 2.9990 chunk 192 optimal weight: 0.0070 chunk 110 optimal weight: 2.9990 chunk 326 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 222 optimal weight: 30.0000 chunk 168 optimal weight: 50.0000 chunk 180 optimal weight: 20.0000 overall best weight: 2.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN H 116 GLN F 116 GLN B 23 GLN B 561 GLN B 999 GLN C 561 GLN C 999 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.188860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.115104 restraints weight = 28121.591| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.00 r_work: 0.3109 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 31206 Z= 0.109 Angle : 0.509 10.679 42549 Z= 0.265 Chirality : 0.044 0.153 4887 Planarity : 0.003 0.036 5406 Dihedral : 4.829 49.217 4779 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.37 % Allowed : 11.91 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.13), residues: 3813 helix: 2.37 (0.20), residues: 693 sheet: 0.49 (0.16), residues: 975 loop : -0.40 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 36 HIS 0.005 0.001 HIS A 516 PHE 0.015 0.001 PHE C 562 TYR 0.017 0.001 TYR A1064 ARG 0.009 0.000 ARG B 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 30) link_NAG-ASN : angle 2.89443 ( 90) hydrogen bonds : bond 0.04433 ( 1292) hydrogen bonds : angle 5.34833 ( 3486) SS BOND : bond 0.00162 ( 51) SS BOND : angle 0.53800 ( 102) covalent geometry : bond 0.00231 (31125) covalent geometry : angle 0.49215 (42357) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 3.697 Fit side-chains REVERT: A 316 ARG cc_start: 0.7536 (mtt-85) cc_final: 0.7253 (mpt90) REVERT: A 437 LYS cc_start: 0.8226 (mttt) cc_final: 0.7970 (mtpt) REVERT: A 455 LYS cc_start: 0.8496 (mmtt) cc_final: 0.7863 (mtmm) REVERT: A 490 ARG cc_start: 0.7270 (mmt90) cc_final: 0.6978 (tpp-160) REVERT: A 643 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7649 (mtp180) REVERT: A 961 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7988 (mppt) REVERT: L 40 GLN cc_start: 0.6532 (OUTLIER) cc_final: 0.4321 (tp40) REVERT: E 87 ASP cc_start: 0.6764 (OUTLIER) cc_final: 0.6153 (m-30) REVERT: B 150 MET cc_start: 0.6338 (OUTLIER) cc_final: 0.5925 (mpt) REVERT: B 318 GLN cc_start: 0.8190 (mm110) cc_final: 0.7951 (mm110) REVERT: B 332 LEU cc_start: 0.8058 (mm) cc_final: 0.7820 (mm) REVERT: B 437 LYS cc_start: 0.8243 (mttt) cc_final: 0.7965 (mtpt) REVERT: B 643 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7122 (mpp-170) REVERT: B 776 GLN cc_start: 0.8989 (tt0) cc_final: 0.8508 (tp40) REVERT: B 847 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7730 (mp) REVERT: B 932 GLN cc_start: 0.7980 (tt0) cc_final: 0.7720 (tt0) REVERT: B 1070 LYS cc_start: 0.8724 (mttt) cc_final: 0.8188 (mptt) REVERT: B 1089 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7942 (pp20) REVERT: C 138 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6929 (mp) REVERT: C 150 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.5392 (pp-130) REVERT: C 169 SER cc_start: 0.7181 (OUTLIER) cc_final: 0.6979 (m) REVERT: C 332 LEU cc_start: 0.7870 (mm) cc_final: 0.7495 (mm) REVERT: C 437 LYS cc_start: 0.8225 (mttt) cc_final: 0.7982 (mtpt) REVERT: C 643 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7580 (mtp180) REVERT: C 742 ASP cc_start: 0.8233 (p0) cc_final: 0.7998 (p0) REVERT: C 776 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8563 (tt0) REVERT: C 1070 LYS cc_start: 0.8730 (mttt) cc_final: 0.8339 (mtpp) outliers start: 46 outliers final: 25 residues processed: 272 average time/residue: 1.3679 time to fit residues: 443.6547 Evaluate side-chains 268 residues out of total 3351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 643 ARG Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 961 LYS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 252 optimal weight: 8.9990 chunk 168 optimal weight: 50.0000 chunk 133 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 188 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 240 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 340 optimal weight: 0.9980 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN A 610 GLN A 999 GLN H 116 GLN F 116 GLN B 561 GLN C 561 GLN C 999 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.187009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.115020 restraints weight = 27872.386| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.17 r_work: 0.3035 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31206 Z= 0.190 Angle : 0.585 10.825 42549 Z= 0.309 Chirality : 0.047 0.175 4887 Planarity : 0.004 0.044 5406 Dihedral : 5.294 50.790 4779 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.37 % Allowed : 11.91 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.13), residues: 3813 helix: 2.11 (0.20), residues: 693 sheet: 0.42 (0.16), residues: 975 loop : -0.49 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 36 HIS 0.007 0.001 HIS A 516 PHE 0.019 0.002 PHE B 895 TYR 0.020 0.002 TYR A1064 ARG 0.011 0.001 ARG B 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 30) link_NAG-ASN : angle 3.01333 ( 90) hydrogen bonds : bond 0.05515 ( 1292) hydrogen bonds : angle 5.66689 ( 3486) SS BOND : bond 0.00306 ( 51) SS BOND : angle 0.76189 ( 102) covalent geometry : bond 0.00431 (31125) covalent geometry : angle 0.56837 (42357) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35374.65 seconds wall clock time: 608 minutes 2.20 seconds (36482.20 seconds total)