Starting phenix.real_space_refine on Fri Mar 6 06:57:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q9g_13869/03_2026/7q9g_13869.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q9g_13869/03_2026/7q9g_13869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q9g_13869/03_2026/7q9g_13869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q9g_13869/03_2026/7q9g_13869.map" model { file = "/net/cci-nas-00/data/ceres_data/7q9g_13869/03_2026/7q9g_13869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q9g_13869/03_2026/7q9g_13869.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.034 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 128 5.16 5 C 18420 2.51 5 N 4771 2.21 5 O 5654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28973 Number of models: 1 Model: "" Number of chains: 22 Chain: "B" Number of atoms: 8281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8281 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 6 Chain: "C" Number of atoms: 8273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8273 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 53, 'TRANS': 1005} Chain breaks: 6 Chain: "A" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8287 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 54, 'TRANS': 1006} Chain breaks: 6 Chain: "H" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 889 Classifications: {'peptide': 119} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 98} Chain: "E" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 889 Classifications: {'peptide': 119} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 114} Chain: "F" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 98} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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 Time building chain proxies: 6.12, per 1000 atoms: 0.21 Number of scatterers: 28973 At special positions: 0 Unit cell: (150.384, 159.783, 215.454, 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 128 16.00 O 5654 8.00 N 4771 7.00 C 18420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " 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=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 328 " " NAG A1304 " - " ASN A 600 " " NAG A1305 " - " ASN A 613 " " NAG A1306 " - " ASN A 654 " " NAG A1307 " - " ASN A 706 " " NAG A1308 " - " ASN A1071 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 340 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 328 " " NAG B1304 " - " ASN B 600 " " NAG B1305 " - " ASN B 613 " " NAG B1306 " - " ASN B 654 " " NAG B1307 " - " ASN B 706 " " NAG B1308 " - " ASN B1071 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 340 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 600 " " NAG C1304 " - " ASN C 613 " " NAG C1305 " - " ASN C 654 " " NAG C1306 " - " ASN C 706 " " NAG C1307 " - " ASN C1071 " " NAG C1308 " - " ASN C 340 " " NAG D 1 " - " ASN B 714 " " NAG G 1 " - " ASN B 798 " " NAG I 1 " - " ASN B1095 " " NAG J 1 " - " ASN B1131 " " NAG K 1 " - " ASN C 714 " " NAG M 1 " - " ASN C 798 " " NAG N 1 " - " ASN C1095 " " NAG O 1 " - " ASN C1131 " " NAG P 1 " - " ASN A 714 " " NAG Q 1 " - " ASN A 798 " " NAG R 1 " - " ASN A1095 " " NAG S 1 " - " ASN A1131 " Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.2 seconds 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6738 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 63 sheets defined 22.6% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.803A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.934A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.835A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 removed outlier: 3.602A pdb=" N ILE B 906 " --> pdb=" O ARG B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.224A 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 1029 removed outlier: 4.466A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.954A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 381 through 387 removed outlier: 3.781A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.095A pdb=" N ARG C 405 " --> pdb=" O ASP 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 734 through 740 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: 3.671A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 910 through 916 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 1029 removed outlier: 4.408A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.751A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.651A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.803A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.632A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 910 through 938 removed outlier: 3.507A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 918 " --> pdb=" O TYR A 914 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 938 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.532A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) 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 removed outlier: 3.612A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1029 removed outlier: 4.874A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 3.673A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.626A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.981A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.005A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.359A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.413A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.863A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.005A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N SER B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL B 143 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.416A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 322 through 325 removed outlier: 6.778A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AB1, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.738A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AB3, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AB4, first strand: chain 'B' and resid 661 through 664 removed outlier: 6.509A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 699 through 701 removed outlier: 3.765A pdb=" N LYS C 787 " --> pdb=" O ASN B 700 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 709 through 712 Processing sheet with id=AB7, first strand: chain 'B' and resid 715 through 725 removed outlier: 6.935A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.371A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 785 through 787 removed outlier: 5.831A pdb=" N ILE B 785 " --> pdb=" O ASN A 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.863A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AC3, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.110A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 260 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.731A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.520A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.373A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.419A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.520A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR C 145 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.413A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 322 through 325 removed outlier: 5.225A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE C 562 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.852A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.599A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AD3, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AD4, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.587A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 708 through 712 Processing sheet with id=AD6, first strand: chain 'C' and resid 715 through 725 removed outlier: 7.093A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AD8, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.584A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AE1, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AE2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.726A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 260 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.865A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.819A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N SER A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 143 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.493A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 322 through 325 Processing sheet with id=AE8, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AE9, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.643A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AF2, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AF3, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.427A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AF5, first strand: chain 'A' and resid 715 through 725 removed outlier: 7.069A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.589A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.520A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.220A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.862A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA L 85 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.862A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA L 85 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AG6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.245A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 4 through 7 removed outlier: 5.044A pdb=" N THR F 70 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N GLN F 27 " --> pdb=" O SER F 68 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N SER F 68 " --> pdb=" O GLN F 27 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N VAL F 29 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N SER F 66 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 13 removed outlier: 5.873A pdb=" N LEU F 11 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 10 through 13 removed outlier: 5.873A pdb=" N LEU F 11 " --> pdb=" O ASP F 105 " (cutoff:3.500A) 1243 hydrogen bonds defined for protein. 3354 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: 6.98 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9232 1.34 - 1.46: 7379 1.46 - 1.58: 12859 1.58 - 1.70: 0 1.70 - 1.82: 164 Bond restraints: 29634 Sorted by residual: bond pdb=" N GLU E 1 " pdb=" CA GLU E 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.72e+00 ... (remaining 29629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 38408 0.97 - 1.94: 1426 1.94 - 2.91: 310 2.91 - 3.88: 153 3.88 - 4.85: 22 Bond angle restraints: 40319 Sorted by residual: angle pdb=" N ASP L 93 " pdb=" CA ASP L 93 " pdb=" C ASP L 93 " ideal model delta sigma weight residual 112.93 109.32 3.61 1.33e+00 5.65e-01 7.35e+00 angle pdb=" N ASP F 93 " pdb=" CA ASP F 93 " pdb=" C ASP F 93 " ideal model delta sigma weight residual 112.93 109.41 3.52 1.33e+00 5.65e-01 6.99e+00 angle pdb=" CA GLY A 413 " pdb=" C GLY A 413 " pdb=" N ASN A 414 " ideal model delta sigma weight residual 114.52 117.27 -2.75 1.09e+00 8.42e-01 6.35e+00 angle pdb=" N ILE B 407 " pdb=" CA ILE B 407 " pdb=" C ILE B 407 " ideal model delta sigma weight residual 106.21 108.82 -2.61 1.07e+00 8.73e-01 5.94e+00 angle pdb=" N GLY B 590 " pdb=" CA GLY B 590 " pdb=" C GLY B 590 " ideal model delta sigma weight residual 110.63 113.76 -3.13 1.45e+00 4.76e-01 4.67e+00 ... (remaining 40314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 17496 17.73 - 35.47: 565 35.47 - 53.20: 164 53.20 - 70.94: 42 70.94 - 88.67: 9 Dihedral angle restraints: 18276 sinusoidal: 7763 harmonic: 10513 Sorted by residual: dihedral pdb=" CA THR A 596 " pdb=" C THR A 596 " pdb=" N PRO A 597 " pdb=" CA PRO A 597 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CB CYS C1079 " pdb=" SG CYS C1079 " pdb=" SG CYS C1123 " pdb=" CB CYS C1123 " ideal model delta sinusoidal sigma weight residual -86.00 -115.14 29.14 1 1.00e+01 1.00e-02 1.21e+01 dihedral pdb=" CA THR B 596 " pdb=" C THR B 596 " pdb=" N PRO B 597 " pdb=" CA PRO B 597 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 18273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2748 0.028 - 0.057: 1259 0.057 - 0.085: 264 0.085 - 0.113: 312 0.113 - 0.142: 110 Chirality restraints: 4693 Sorted by residual: chirality pdb=" CA ILE C 119 " pdb=" N ILE C 119 " pdb=" C ILE C 119 " pdb=" CB ILE C 119 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE B 128 " pdb=" N ILE B 128 " pdb=" C ILE B 128 " pdb=" CB ILE B 128 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE C 203 " pdb=" N ILE C 203 " pdb=" C ILE C 203 " pdb=" CB ILE C 203 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 4690 not shown) Planarity restraints: 5193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A1086 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO A1087 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A1087 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1087 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 957 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C ASN A 957 " -0.023 2.00e-02 2.50e+03 pdb=" O ASN A 957 " 0.009 2.00e-02 2.50e+03 pdb=" N THR A 958 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 952 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C ASN B 952 " -0.023 2.00e-02 2.50e+03 pdb=" O ASN B 952 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA B 953 " 0.008 2.00e-02 2.50e+03 ... (remaining 5190 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 320 2.61 - 3.18: 25687 3.18 - 3.75: 43817 3.75 - 4.33: 64123 4.33 - 4.90: 107060 Nonbonded interactions: 241007 Sorted by model distance: nonbonded pdb=" OD1 ASN A 537 " pdb=" OG1 THR A 546 " model vdw 2.034 3.040 nonbonded pdb=" OD2 ASP B 575 " pdb=" OG1 THR B 578 " model vdw 2.039 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.044 3.040 nonbonded pdb=" O ASN B 436 " pdb=" OG SER B 440 " model vdw 2.070 3.040 nonbonded pdb=" O ASN A 436 " pdb=" OG SER A 440 " model vdw 2.079 3.040 ... (remaining 241002 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 617 or resid 638 through 1308)) selection = (chain 'B' and (resid 13 through 617 or resid 638 through 1308)) selection = (chain 'C' and (resid 13 through 617 or resid 638 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' 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: 8.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 27.400 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 : 0.003 0.034 29732 Z= 0.165 Angle : 0.503 4.852 40567 Z= 0.257 Chirality : 0.043 0.142 4693 Planarity : 0.003 0.034 5153 Dihedral : 10.010 88.670 11400 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.67 % Allowed : 3.46 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.14), residues: 3582 helix: 0.71 (0.21), residues: 701 sheet: 0.03 (0.16), residues: 938 loop : -0.28 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1016 TYR 0.014 0.001 TYR B1064 PHE 0.014 0.001 PHE C 756 TRP 0.008 0.001 TRP B 883 HIS 0.003 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00337 (29634) covalent geometry : angle 0.49724 (40319) SS BOND : bond 0.00193 ( 46) SS BOND : angle 0.64523 ( 92) hydrogen bonds : bond 0.12315 ( 1188) hydrogen bonds : angle 6.88244 ( 3354) link_BETA1-4 : bond 0.00188 ( 12) link_BETA1-4 : angle 0.88817 ( 36) link_NAG-ASN : bond 0.00144 ( 40) link_NAG-ASN : angle 1.36933 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 353 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 GLU cc_start: 0.5596 (OUTLIER) cc_final: 0.5358 (pm20) REVERT: B 133 PHE cc_start: 0.7463 (m-80) cc_final: 0.7164 (m-80) REVERT: B 205 SER cc_start: 0.8601 (p) cc_final: 0.7868 (p) REVERT: B 820 PHE cc_start: 0.7456 (m-80) cc_final: 0.7212 (m-10) REVERT: B 978 LEU cc_start: 0.8534 (mt) cc_final: 0.8308 (mm) REVERT: C 562 PHE cc_start: 0.7277 (p90) cc_final: 0.6066 (p90) REVERT: C 564 ARG cc_start: 0.5982 (mtt-85) cc_final: 0.5732 (mtt-85) REVERT: C 853 ASN cc_start: 0.8341 (t0) cc_final: 0.8057 (t0) REVERT: A 86 PHE cc_start: 0.8402 (t80) cc_final: 0.7759 (t80) REVERT: A 281 THR cc_start: 0.8339 (m) cc_final: 0.8134 (p) REVERT: H 80 LEU cc_start: 0.5504 (tp) cc_final: 0.4499 (tp) REVERT: L 4 MET cc_start: -0.0224 (mmt) cc_final: -0.1239 (mtm) REVERT: F 4 MET cc_start: -0.1786 (mmt) cc_final: -0.3123 (mtt) outliers start: 21 outliers final: 11 residues processed: 372 average time/residue: 0.1882 time to fit residues: 111.9220 Evaluate side-chains 209 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1119 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0470 chunk 298 optimal weight: 2.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 207 HIS B 759 GLN B1103 GLN ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN C 869 GLN C 932 GLN C 975 ASN A 207 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.180308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.119804 restraints weight = 56345.533| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 4.39 r_work: 0.3227 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29732 Z= 0.140 Angle : 0.566 12.486 40567 Z= 0.290 Chirality : 0.044 0.218 4693 Planarity : 0.004 0.068 5153 Dihedral : 6.566 88.751 5017 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.81 % Allowed : 6.93 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3582 helix: 1.45 (0.19), residues: 702 sheet: 0.19 (0.16), residues: 970 loop : -0.32 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 992 TYR 0.024 0.001 TYR B1064 PHE 0.020 0.001 PHE B 326 TRP 0.011 0.001 TRP H 105 HIS 0.014 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00317 (29634) covalent geometry : angle 0.55344 (40319) SS BOND : bond 0.00305 ( 46) SS BOND : angle 1.73521 ( 92) hydrogen bonds : bond 0.03927 ( 1188) hydrogen bonds : angle 5.43820 ( 3354) link_BETA1-4 : bond 0.00313 ( 12) link_BETA1-4 : angle 0.97404 ( 36) link_NAG-ASN : bond 0.00235 ( 40) link_NAG-ASN : angle 1.66473 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 214 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 820 PHE cc_start: 0.7815 (m-80) cc_final: 0.7514 (m-10) REVERT: C 160 TYR cc_start: 0.8472 (p90) cc_final: 0.8106 (p90) REVERT: C 229 LEU cc_start: 0.8291 (mt) cc_final: 0.8007 (mp) REVERT: C 556 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7600 (t80) REVERT: C 562 PHE cc_start: 0.7476 (p90) cc_final: 0.6840 (p90) REVERT: C 814 PHE cc_start: 0.8570 (t80) cc_final: 0.8361 (t80) REVERT: C 853 ASN cc_start: 0.8652 (t0) cc_final: 0.8432 (t0) REVERT: C 947 ASP cc_start: 0.8085 (t0) cc_final: 0.7882 (t0) REVERT: A 86 PHE cc_start: 0.8609 (t80) cc_final: 0.7766 (t80) REVERT: A 168 PHE cc_start: 0.8219 (t80) cc_final: 0.7996 (t80) REVERT: A 281 THR cc_start: 0.8520 (m) cc_final: 0.8252 (p) REVERT: A 293 LEU cc_start: 0.8640 (tp) cc_final: 0.8425 (tt) REVERT: H 34 MET cc_start: 0.8842 (mmm) cc_final: 0.8329 (mmm) REVERT: L 97 ARG cc_start: 0.8904 (mmt180) cc_final: 0.8429 (ttp80) REVERT: F 4 MET cc_start: 0.0056 (mmt) cc_final: -0.1336 (mtt) outliers start: 57 outliers final: 33 residues processed: 257 average time/residue: 0.1601 time to fit residues: 70.3480 Evaluate side-chains 205 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1139 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 11 optimal weight: 9.9990 chunk 320 optimal weight: 50.0000 chunk 218 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 355 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 348 optimal weight: 40.0000 chunk 67 optimal weight: 7.9990 chunk 328 optimal weight: 30.0000 chunk 113 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 311 GLN B 610 GLN B 748 ASN B 781 GLN B 932 GLN C 898 GLN C 952 ASN ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.177193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.126318 restraints weight = 56509.367| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.22 r_work: 0.3173 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 29732 Z= 0.308 Angle : 0.631 11.630 40567 Z= 0.323 Chirality : 0.046 0.233 4693 Planarity : 0.004 0.060 5153 Dihedral : 6.011 59.618 5009 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.54 % Allowed : 7.60 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3582 helix: 1.39 (0.20), residues: 680 sheet: 0.07 (0.16), residues: 970 loop : -0.46 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 564 TYR 0.026 0.002 TYR B1064 PHE 0.023 0.002 PHE B 192 TRP 0.020 0.002 TRP B 152 HIS 0.009 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00717 (29634) covalent geometry : angle 0.61437 (40319) SS BOND : bond 0.00389 ( 46) SS BOND : angle 2.23830 ( 92) hydrogen bonds : bond 0.04314 ( 1188) hydrogen bonds : angle 5.53556 ( 3354) link_BETA1-4 : bond 0.00236 ( 12) link_BETA1-4 : angle 1.21715 ( 36) link_NAG-ASN : bond 0.00407 ( 40) link_NAG-ASN : angle 1.85383 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 185 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 THR cc_start: 0.7825 (m) cc_final: 0.7423 (p) REVERT: B 311 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7049 (tp-100) REVERT: C 160 TYR cc_start: 0.8609 (p90) cc_final: 0.8186 (p90) REVERT: C 229 LEU cc_start: 0.8159 (mt) cc_final: 0.7669 (mp) REVERT: C 556 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7640 (t80) REVERT: C 737 MET cc_start: 0.8130 (mtp) cc_final: 0.7878 (mtp) REVERT: C 853 ASN cc_start: 0.8687 (t0) cc_final: 0.8419 (t0) REVERT: C 947 ASP cc_start: 0.8129 (t0) cc_final: 0.7860 (t0) REVERT: A 86 PHE cc_start: 0.8597 (t80) cc_final: 0.7917 (t80) REVERT: A 281 THR cc_start: 0.8602 (m) cc_final: 0.8350 (p) REVERT: L 97 ARG cc_start: 0.8669 (mmt180) cc_final: 0.8305 (ttp80) REVERT: F 4 MET cc_start: -0.0594 (mmt) cc_final: -0.1994 (mtt) outliers start: 80 outliers final: 61 residues processed: 243 average time/residue: 0.1645 time to fit residues: 67.3737 Evaluate side-chains 226 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 163 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 952 ASN Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 105 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 306 optimal weight: 0.9980 chunk 284 optimal weight: 0.9980 chunk 180 optimal weight: 0.0670 chunk 193 optimal weight: 0.5980 chunk 0 optimal weight: 40.0000 chunk 69 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 229 optimal weight: 10.0000 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 GLN B 932 GLN B 952 ASN B1103 GLN C 561 GLN C 610 GLN C 898 GLN C 952 ASN C 989 GLN A 218 GLN A 752 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.179107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.119353 restraints weight = 56230.047| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 4.50 r_work: 0.3219 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 29732 Z= 0.119 Angle : 0.537 12.567 40567 Z= 0.275 Chirality : 0.043 0.245 4693 Planarity : 0.004 0.050 5153 Dihedral : 5.482 58.358 5009 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.91 % Allowed : 8.80 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3582 helix: 1.78 (0.20), residues: 681 sheet: 0.20 (0.16), residues: 965 loop : -0.37 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 102 TYR 0.019 0.001 TYR B1064 PHE 0.029 0.001 PHE B 192 TRP 0.040 0.001 TRP L 36 HIS 0.004 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00268 (29634) covalent geometry : angle 0.52117 (40319) SS BOND : bond 0.00278 ( 46) SS BOND : angle 2.07631 ( 92) hydrogen bonds : bond 0.03555 ( 1188) hydrogen bonds : angle 5.24404 ( 3354) link_BETA1-4 : bond 0.00263 ( 12) link_BETA1-4 : angle 1.02690 ( 36) link_NAG-ASN : bond 0.00203 ( 40) link_NAG-ASN : angle 1.60508 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 239 GLN cc_start: 0.7377 (tt0) cc_final: 0.7117 (tp-100) REVERT: B 311 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7369 (tp-100) REVERT: C 160 TYR cc_start: 0.8442 (p90) cc_final: 0.8092 (p90) REVERT: C 556 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7534 (t80) REVERT: C 737 MET cc_start: 0.8032 (mtp) cc_final: 0.7817 (mtp) REVERT: C 814 PHE cc_start: 0.8625 (t80) cc_final: 0.8404 (t80) REVERT: C 853 ASN cc_start: 0.8623 (t0) cc_final: 0.8416 (t0) REVERT: C 947 ASP cc_start: 0.8119 (t0) cc_final: 0.7844 (t0) REVERT: A 86 PHE cc_start: 0.8554 (t80) cc_final: 0.7881 (t80) REVERT: A 177 MET cc_start: -0.4940 (ttt) cc_final: -0.6984 (mmt) REVERT: A 281 THR cc_start: 0.8605 (m) cc_final: 0.8376 (p) REVERT: F 4 MET cc_start: -0.0104 (mmt) cc_final: -0.1463 (mtt) outliers start: 60 outliers final: 48 residues processed: 228 average time/residue: 0.1661 time to fit residues: 64.4651 Evaluate side-chains 221 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 952 ASN Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 47 optimal weight: 50.0000 chunk 136 optimal weight: 0.4980 chunk 69 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 227 optimal weight: 9.9990 chunk 256 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 352 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 257 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 GLN C 761 ASN C 952 ASN A 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.177843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.127923 restraints weight = 56058.135| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.82 r_work: 0.3242 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29732 Z= 0.210 Angle : 0.558 13.064 40567 Z= 0.285 Chirality : 0.044 0.203 4693 Planarity : 0.004 0.062 5153 Dihedral : 5.262 59.051 5006 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.42 % Allowed : 9.22 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3582 helix: 1.58 (0.20), residues: 685 sheet: 0.26 (0.16), residues: 951 loop : -0.39 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 97 TYR 0.022 0.001 TYR B1064 PHE 0.017 0.001 PHE B 65 TRP 0.036 0.002 TRP L 36 HIS 0.004 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00487 (29634) covalent geometry : angle 0.54320 (40319) SS BOND : bond 0.00402 ( 46) SS BOND : angle 2.04863 ( 92) hydrogen bonds : bond 0.03764 ( 1188) hydrogen bonds : angle 5.29087 ( 3354) link_BETA1-4 : bond 0.00208 ( 12) link_BETA1-4 : angle 1.07895 ( 36) link_NAG-ASN : bond 0.00251 ( 40) link_NAG-ASN : angle 1.65458 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 180 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 THR cc_start: 0.8013 (m) cc_final: 0.7536 (p) REVERT: B 239 GLN cc_start: 0.7742 (tt0) cc_final: 0.7501 (tp40) REVERT: B 311 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7799 (tp-100) REVERT: B 529 ASN cc_start: 0.8523 (t0) cc_final: 0.8254 (t0) REVERT: C 160 TYR cc_start: 0.8558 (p90) cc_final: 0.8215 (p90) REVERT: C 556 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7585 (t80) REVERT: C 737 MET cc_start: 0.8350 (mtp) cc_final: 0.8111 (mtp) REVERT: C 853 ASN cc_start: 0.8800 (t0) cc_final: 0.8523 (t0) REVERT: C 947 ASP cc_start: 0.8372 (t0) cc_final: 0.8050 (t0) REVERT: A 86 PHE cc_start: 0.8664 (t80) cc_final: 0.7931 (t80) REVERT: A 177 MET cc_start: -0.5028 (ttt) cc_final: -0.6894 (mmt) REVERT: A 855 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8640 (mt) REVERT: F 4 MET cc_start: -0.0643 (mmt) cc_final: -0.2098 (mtt) outliers start: 76 outliers final: 60 residues processed: 236 average time/residue: 0.1590 time to fit residues: 64.1245 Evaluate side-chains 225 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 162 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 952 ASN Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 320 optimal weight: 20.0000 chunk 185 optimal weight: 1.9990 chunk 246 optimal weight: 0.0170 chunk 120 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 23 optimal weight: 0.0570 chunk 77 optimal weight: 0.0000 chunk 207 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 218 optimal weight: 8.9990 chunk 276 optimal weight: 0.9990 overall best weight: 0.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 357 ASN ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 999 GLN A1051 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.179419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.119763 restraints weight = 55944.917| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 4.49 r_work: 0.3236 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 29732 Z= 0.108 Angle : 0.516 10.500 40567 Z= 0.262 Chirality : 0.043 0.210 4693 Planarity : 0.003 0.045 5153 Dihedral : 4.871 59.763 5006 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.91 % Allowed : 10.08 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3582 helix: 1.86 (0.20), residues: 673 sheet: 0.32 (0.16), residues: 961 loop : -0.30 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 97 TYR 0.019 0.001 TYR B1064 PHE 0.025 0.001 PHE B 192 TRP 0.023 0.001 TRP L 36 HIS 0.003 0.000 HIS B1085 Details of bonding type rmsd covalent geometry : bond 0.00239 (29634) covalent geometry : angle 0.50481 (40319) SS BOND : bond 0.00638 ( 46) SS BOND : angle 1.52500 ( 92) hydrogen bonds : bond 0.03367 ( 1188) hydrogen bonds : angle 5.10685 ( 3354) link_BETA1-4 : bond 0.00241 ( 12) link_BETA1-4 : angle 0.96580 ( 36) link_NAG-ASN : bond 0.00184 ( 40) link_NAG-ASN : angle 1.51040 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 175 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.2697 (ttt) cc_final: -0.4385 (tpt) REVERT: B 239 GLN cc_start: 0.7434 (tt0) cc_final: 0.7139 (tp40) REVERT: B 311 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7319 (tp40) REVERT: C 160 TYR cc_start: 0.8437 (p90) cc_final: 0.8145 (p90) REVERT: C 205 SER cc_start: 0.8914 (p) cc_final: 0.8686 (p) REVERT: C 556 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7556 (t80) REVERT: C 737 MET cc_start: 0.8054 (mtp) cc_final: 0.7792 (mtp) REVERT: C 814 PHE cc_start: 0.8602 (t80) cc_final: 0.8375 (t80) REVERT: C 947 ASP cc_start: 0.8097 (t0) cc_final: 0.7833 (t0) REVERT: A 86 PHE cc_start: 0.8549 (t80) cc_final: 0.7873 (t80) REVERT: A 153 MET cc_start: 0.8453 (mmm) cc_final: 0.8122 (mmm) REVERT: A 177 MET cc_start: -0.5302 (ttt) cc_final: -0.6997 (mmt) REVERT: A 855 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8560 (mt) REVERT: F 4 MET cc_start: -0.0392 (mmt) cc_final: -0.1802 (mtt) outliers start: 60 outliers final: 45 residues processed: 217 average time/residue: 0.1619 time to fit residues: 60.5353 Evaluate side-chains 208 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 4 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 288 optimal weight: 4.9990 chunk 184 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 243 optimal weight: 40.0000 chunk 276 optimal weight: 1.9990 chunk 324 optimal weight: 9.9990 chunk 205 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.177704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.116270 restraints weight = 56238.920| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 4.55 r_work: 0.3170 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 29732 Z= 0.215 Angle : 0.560 10.820 40567 Z= 0.283 Chirality : 0.044 0.237 4693 Planarity : 0.004 0.040 5153 Dihedral : 4.831 58.031 5006 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.19 % Allowed : 10.27 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3582 helix: 1.61 (0.20), residues: 672 sheet: 0.32 (0.16), residues: 958 loop : -0.36 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 97 TYR 0.022 0.001 TYR B1064 PHE 0.017 0.001 PHE B 65 TRP 0.019 0.001 TRP L 36 HIS 0.005 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00500 (29634) covalent geometry : angle 0.54673 (40319) SS BOND : bond 0.00325 ( 46) SS BOND : angle 1.79338 ( 92) hydrogen bonds : bond 0.03771 ( 1188) hydrogen bonds : angle 5.20637 ( 3354) link_BETA1-4 : bond 0.00177 ( 12) link_BETA1-4 : angle 1.10537 ( 36) link_NAG-ASN : bond 0.00264 ( 40) link_NAG-ASN : angle 1.62493 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 172 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.2740 (ttt) cc_final: -0.4475 (tpt) REVERT: B 239 GLN cc_start: 0.7483 (tt0) cc_final: 0.7147 (tp40) REVERT: B 529 ASN cc_start: 0.8623 (t0) cc_final: 0.8332 (t0) REVERT: B 657 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.8478 (m-80) REVERT: C 160 TYR cc_start: 0.8506 (p90) cc_final: 0.8177 (p90) REVERT: C 229 LEU cc_start: 0.8322 (tt) cc_final: 0.7834 (mm) REVERT: C 556 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7625 (t80) REVERT: C 737 MET cc_start: 0.8150 (mtp) cc_final: 0.7905 (mtp) REVERT: C 947 ASP cc_start: 0.8159 (t0) cc_final: 0.7895 (t0) REVERT: C 1141 GLU cc_start: 0.8314 (mp0) cc_final: 0.8074 (mp0) REVERT: A 86 PHE cc_start: 0.8541 (t80) cc_final: 0.7866 (t80) REVERT: A 177 MET cc_start: -0.5040 (ttt) cc_final: -0.6964 (mmt) REVERT: A 855 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8666 (mt) REVERT: A 980 ARG cc_start: 0.8473 (mtm180) cc_final: 0.7909 (ttp-170) REVERT: L 4 MET cc_start: 0.3631 (mtm) cc_final: 0.3261 (ttm) REVERT: F 4 MET cc_start: -0.0143 (mmt) cc_final: -0.1425 (mtt) outliers start: 69 outliers final: 59 residues processed: 225 average time/residue: 0.1685 time to fit residues: 64.8043 Evaluate side-chains 222 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 160 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 156 optimal weight: 20.0000 chunk 165 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 327 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 189 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 170 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 247 optimal weight: 30.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.179039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.116849 restraints weight = 56097.524| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 4.34 r_work: 0.3202 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29732 Z= 0.128 Angle : 0.531 10.801 40567 Z= 0.268 Chirality : 0.043 0.219 4693 Planarity : 0.003 0.041 5153 Dihedral : 4.636 55.851 5006 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.03 % Allowed : 10.81 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.14), residues: 3582 helix: 1.91 (0.20), residues: 654 sheet: 0.41 (0.17), residues: 965 loop : -0.32 (0.14), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 97 TYR 0.028 0.001 TYR H 94 PHE 0.028 0.001 PHE B 168 TRP 0.016 0.001 TRP H 36 HIS 0.003 0.001 HIS B1085 Details of bonding type rmsd covalent geometry : bond 0.00293 (29634) covalent geometry : angle 0.51724 (40319) SS BOND : bond 0.00262 ( 46) SS BOND : angle 1.87711 ( 92) hydrogen bonds : bond 0.03426 ( 1188) hydrogen bonds : angle 5.04466 ( 3354) link_BETA1-4 : bond 0.00253 ( 12) link_BETA1-4 : angle 1.01128 ( 36) link_NAG-ASN : bond 0.00177 ( 40) link_NAG-ASN : angle 1.50329 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 170 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.2502 (ttt) cc_final: -0.4352 (tpt) REVERT: B 239 GLN cc_start: 0.7441 (tt0) cc_final: 0.7109 (tp40) REVERT: B 529 ASN cc_start: 0.8571 (t0) cc_final: 0.8272 (t0) REVERT: B 657 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.8442 (m-80) REVERT: B 975 ASN cc_start: 0.8431 (t0) cc_final: 0.7981 (t0) REVERT: C 160 TYR cc_start: 0.8374 (p90) cc_final: 0.8084 (p90) REVERT: C 556 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7647 (t80) REVERT: C 737 MET cc_start: 0.8117 (mtp) cc_final: 0.7881 (mtp) REVERT: C 814 PHE cc_start: 0.8636 (t80) cc_final: 0.8388 (t80) REVERT: C 947 ASP cc_start: 0.8138 (t0) cc_final: 0.7879 (t0) REVERT: A 86 PHE cc_start: 0.8584 (t80) cc_final: 0.7860 (t80) REVERT: A 177 MET cc_start: -0.5011 (ttt) cc_final: -0.6991 (mmt) REVERT: A 855 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8626 (mt) REVERT: A 980 ARG cc_start: 0.8489 (mtm180) cc_final: 0.8253 (mtp180) REVERT: L 4 MET cc_start: 0.4440 (mtm) cc_final: 0.4086 (ttm) REVERT: F 4 MET cc_start: 0.0467 (mmt) cc_final: -0.0808 (mtt) outliers start: 64 outliers final: 56 residues processed: 217 average time/residue: 0.1685 time to fit residues: 62.5511 Evaluate side-chains 225 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 166 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 290 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 227 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 326 optimal weight: 50.0000 chunk 60 optimal weight: 0.4980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.178176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.118241 restraints weight = 56191.867| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 5.07 r_work: 0.3153 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29732 Z= 0.192 Angle : 0.550 10.948 40567 Z= 0.277 Chirality : 0.043 0.191 4693 Planarity : 0.004 0.040 5153 Dihedral : 4.625 50.804 5006 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.23 % Allowed : 10.65 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3582 helix: 1.74 (0.20), residues: 654 sheet: 0.40 (0.17), residues: 953 loop : -0.33 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 97 TYR 0.022 0.001 TYR H 94 PHE 0.023 0.001 PHE B 168 TRP 0.016 0.001 TRP L 36 HIS 0.005 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00444 (29634) covalent geometry : angle 0.53670 (40319) SS BOND : bond 0.00326 ( 46) SS BOND : angle 1.83416 ( 92) hydrogen bonds : bond 0.03649 ( 1188) hydrogen bonds : angle 5.10096 ( 3354) link_BETA1-4 : bond 0.00209 ( 12) link_BETA1-4 : angle 1.08452 ( 36) link_NAG-ASN : bond 0.00225 ( 40) link_NAG-ASN : angle 1.57806 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 168 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.2350 (ttt) cc_final: -0.4303 (tpt) REVERT: B 239 GLN cc_start: 0.7445 (tt0) cc_final: 0.7208 (tp40) REVERT: B 529 ASN cc_start: 0.8391 (t0) cc_final: 0.8105 (t0) REVERT: B 657 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8504 (m-80) REVERT: B 975 ASN cc_start: 0.8494 (t0) cc_final: 0.8083 (t0) REVERT: C 32 PHE cc_start: 0.7796 (m-80) cc_final: 0.7574 (m-80) REVERT: C 160 TYR cc_start: 0.8471 (p90) cc_final: 0.8174 (p90) REVERT: C 556 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7629 (t80) REVERT: C 737 MET cc_start: 0.8171 (mtp) cc_final: 0.7932 (mtp) REVERT: C 947 ASP cc_start: 0.8261 (t0) cc_final: 0.7975 (t0) REVERT: A 86 PHE cc_start: 0.8502 (t80) cc_final: 0.7834 (t80) REVERT: A 177 MET cc_start: -0.4875 (ttt) cc_final: -0.6955 (mmt) REVERT: F 4 MET cc_start: -0.0008 (mmt) cc_final: -0.1335 (mtt) outliers start: 70 outliers final: 62 residues processed: 223 average time/residue: 0.1723 time to fit residues: 65.8489 Evaluate side-chains 224 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 160 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 129 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 153 optimal weight: 50.0000 chunk 263 optimal weight: 0.9990 chunk 158 optimal weight: 9.9990 chunk 226 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 206 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.179406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.117041 restraints weight = 56061.169| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 4.28 r_work: 0.3213 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29732 Z= 0.124 Angle : 0.524 10.972 40567 Z= 0.262 Chirality : 0.042 0.175 4693 Planarity : 0.003 0.039 5153 Dihedral : 4.420 50.470 5006 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.91 % Allowed : 11.03 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3582 helix: 1.92 (0.20), residues: 656 sheet: 0.45 (0.17), residues: 960 loop : -0.29 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 564 TYR 0.030 0.001 TYR H 94 PHE 0.024 0.001 PHE B 168 TRP 0.016 0.001 TRP L 36 HIS 0.002 0.000 HIS B1085 Details of bonding type rmsd covalent geometry : bond 0.00284 (29634) covalent geometry : angle 0.51319 (40319) SS BOND : bond 0.00279 ( 46) SS BOND : angle 1.61020 ( 92) hydrogen bonds : bond 0.03361 ( 1188) hydrogen bonds : angle 4.95984 ( 3354) link_BETA1-4 : bond 0.00279 ( 12) link_BETA1-4 : angle 0.97481 ( 36) link_NAG-ASN : bond 0.00164 ( 40) link_NAG-ASN : angle 1.47789 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 161 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: -0.2809 (ttt) cc_final: -0.4545 (tpt) REVERT: B 239 GLN cc_start: 0.7382 (tt0) cc_final: 0.7086 (tp40) REVERT: B 529 ASN cc_start: 0.8542 (t0) cc_final: 0.8239 (t0) REVERT: B 657 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.8465 (m-80) REVERT: B 975 ASN cc_start: 0.8400 (t0) cc_final: 0.7983 (t0) REVERT: C 32 PHE cc_start: 0.7755 (m-80) cc_final: 0.7528 (m-80) REVERT: C 160 TYR cc_start: 0.8419 (p90) cc_final: 0.8113 (p90) REVERT: C 177 MET cc_start: -0.0053 (mtt) cc_final: -0.0766 (mtt) REVERT: C 205 SER cc_start: 0.8933 (p) cc_final: 0.8685 (p) REVERT: C 556 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7693 (t80) REVERT: C 562 PHE cc_start: 0.7360 (p90) cc_final: 0.6959 (p90) REVERT: C 749 LEU cc_start: 0.8880 (tp) cc_final: 0.8624 (tt) REVERT: C 947 ASP cc_start: 0.8110 (t0) cc_final: 0.7848 (t0) REVERT: A 86 PHE cc_start: 0.8539 (t80) cc_final: 0.7831 (t80) REVERT: A 177 MET cc_start: -0.5228 (ttt) cc_final: -0.6950 (mmt) REVERT: L 4 MET cc_start: 0.3547 (mtm) cc_final: 0.3148 (ttm) REVERT: F 4 MET cc_start: -0.0245 (mmt) cc_final: -0.1567 (mtt) outliers start: 60 outliers final: 54 residues processed: 206 average time/residue: 0.1729 time to fit residues: 60.8580 Evaluate side-chains 212 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 156 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 275 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 102 optimal weight: 0.3980 chunk 135 optimal weight: 10.0000 chunk 295 optimal weight: 1.9990 chunk 285 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 243 optimal weight: 20.0000 chunk 266 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.178653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116285 restraints weight = 56429.766| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 4.51 r_work: 0.3186 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29732 Z= 0.157 Angle : 0.533 10.963 40567 Z= 0.267 Chirality : 0.043 0.169 4693 Planarity : 0.003 0.040 5153 Dihedral : 4.372 50.808 5006 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.03 % Allowed : 11.06 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3582 helix: 1.89 (0.20), residues: 648 sheet: 0.47 (0.17), residues: 969 loop : -0.30 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 564 TYR 0.039 0.001 TYR H 94 PHE 0.023 0.001 PHE B 168 TRP 0.016 0.001 TRP L 36 HIS 0.003 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00363 (29634) covalent geometry : angle 0.52127 (40319) SS BOND : bond 0.00305 ( 46) SS BOND : angle 1.63173 ( 92) hydrogen bonds : bond 0.03484 ( 1188) hydrogen bonds : angle 4.97324 ( 3354) link_BETA1-4 : bond 0.00221 ( 12) link_BETA1-4 : angle 1.03162 ( 36) link_NAG-ASN : bond 0.00178 ( 40) link_NAG-ASN : angle 1.51935 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8972.38 seconds wall clock time: 154 minutes 6.64 seconds (9246.64 seconds total)