Starting phenix.real_space_refine on Tue Apr 7 23:34:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ls9_23506/04_2026/7ls9_23506.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ls9_23506/04_2026/7ls9_23506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ls9_23506/04_2026/7ls9_23506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ls9_23506/04_2026/7ls9_23506.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ls9_23506/04_2026/7ls9_23506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ls9_23506/04_2026/7ls9_23506.map" } resolution = 3.42 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= 0.003 sd= 0.021 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 144 5.16 5 C 20436 2.51 5 N 5304 2.21 5 O 6342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 234 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32226 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8574 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 54, 'TRANS': 1042} Chain breaks: 5 Chain: "H" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "B" Number of atoms: 8574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8574 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 54, 'TRANS': 1042} Chain breaks: 5 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "F" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "C" Number of atoms: 8574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8574 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 54, 'TRANS': 1042} Chain breaks: 5 Chain: "E" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "Z" 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: "a" 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: 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: "c" 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: "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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "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: "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: "U" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "T" 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: "V" 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: "W" 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: "X" 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: "Y" 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 7.49, per 1000 atoms: 0.23 Number of scatterers: 32226 At special positions: 0 Unit cell: (140.17, 140.17, 206.51, 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 144 16.00 O 6342 8.00 N 5304 7.00 C 20436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 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 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100A" - pdb=" SG CYS H 100F" distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 100A" - pdb=" SG CYS D 100F" distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " 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 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 100A" - pdb=" SG CYS E 100F" distance=2.05 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 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 I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 17 " " NAG A1310 " - " ASN A 343 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 17 " " NAG B1310 " - " ASN B 343 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 17 " " NAG C1310 " - " ASN C 343 " " NAG I 1 " - " ASN A 165 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN B 165 " " NAG M 1 " - " ASN B 234 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN C 165 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN C 234 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN B 122 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " " NAG Y 1 " - " ASN C 122 " " NAG Z 1 " - " ASN A 717 " " NAG a 1 " - " ASN A 801 " " NAG b 1 " - " ASN A1098 " " NAG c 1 " - " ASN A1134 " " NAG d 1 " - " ASN A 122 " Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.3 seconds 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7446 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 69 sheets defined 22.5% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.040A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.306A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 749 through 757 Processing helix chain 'A' and resid 757 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 832 through 838 Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.929A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.970A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.254A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.713A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.846A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.215A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.871A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.766A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 31 removed outlier: 4.248A pdb=" N SER L 31 " --> pdb=" O VAL L 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 31' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.090A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.050A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.300A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.650A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 630 through 636 removed outlier: 3.626A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 749 through 757 Processing helix chain 'B' and resid 757 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 832 through 838 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.782A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 889 removed outlier: 3.702A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 889' Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.100A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 968 removed outlier: 3.618A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 968 " --> pdb=" O LYS B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.822A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.006A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.900A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 52A through 54 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.900A pdb=" N THR D 87 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 31 removed outlier: 3.906A pdb=" N SER F 31 " --> pdb=" O VAL F 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 31' Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.077A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.882A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.296A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.737A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 625 Processing helix chain 'C' and resid 630 through 636 removed outlier: 3.601A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 749 through 783 removed outlier: 6.415A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 832 through 838 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.810A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.236A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.174A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.642A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.806A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.287A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.924A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.801A pdb=" N THR E 87 " --> pdb=" O THR E 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 31 removed outlier: 4.202A pdb=" N SER G 31 " --> pdb=" O VAL G 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 31' Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.155A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.083A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.814A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.519A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.996A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.996A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.891A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.616A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.230A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.674A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.674A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.791A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.755A pdb=" N SER H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP H 72 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.647A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.647A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 100 through 100B Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.594A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.511A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.511A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.124A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.806A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.819A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 141 through 144 Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AD3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.008A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.008A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD7, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.192A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.719A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.175A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.676A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.676A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.512A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.733A pdb=" N THR D 107 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 88 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.733A pdb=" N THR D 107 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 88 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 100 through 100B removed outlier: 3.522A pdb=" N ILE D 100B" --> pdb=" O VAL D 100E" (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.587A pdb=" N SER F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.608A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN F 37 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG F 45 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.608A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.124A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.810A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.787A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 141 through 144 Processing sheet with id=AF7, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AF8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.038A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.038A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AG2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AG3, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.750A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.684A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.684A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.794A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 1094 through 1098 Processing sheet with id=AG9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AH1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.912A pdb=" N THR E 107 " --> pdb=" O TYR E 90 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.912A pdb=" N THR E 107 " --> pdb=" O TYR E 90 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 100 through 100B Processing sheet with id=AH4, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.593A pdb=" N SER G 22 " --> pdb=" O SER G 7 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS G 23 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE G 71 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.674A pdb=" N GLN G 89 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN G 37 " --> pdb=" O ARG G 45 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.699A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) 1303 hydrogen bonds defined for protein. 3528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.71 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5373 1.32 - 1.46: 11551 1.46 - 1.59: 15840 1.59 - 1.73: 2 1.73 - 1.86: 180 Bond restraints: 32946 Sorted by residual: bond pdb=" CG PRO F 40 " pdb=" CD PRO F 40 " ideal model delta sigma weight residual 1.503 1.244 0.259 3.40e-02 8.65e+02 5.79e+01 bond pdb=" CG PRO G 59 " pdb=" CD PRO G 59 " ideal model delta sigma weight residual 1.503 1.309 0.194 3.40e-02 8.65e+02 3.26e+01 bond pdb=" CA ALA D 99 " pdb=" CB ALA D 99 " ideal model delta sigma weight residual 1.530 1.463 0.066 1.48e-02 4.57e+03 2.01e+01 bond pdb=" CA ALA H 99 " pdb=" CB ALA H 99 " ideal model delta sigma weight residual 1.529 1.462 0.067 1.66e-02 3.63e+03 1.61e+01 bond pdb=" C PHE E 100G" pdb=" O PHE E 100G" ideal model delta sigma weight residual 1.236 1.189 0.046 1.17e-02 7.31e+03 1.58e+01 ... (remaining 32941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 44321 3.29 - 6.58: 435 6.58 - 9.88: 50 9.88 - 13.17: 4 13.17 - 16.46: 4 Bond angle restraints: 44814 Sorted by residual: angle pdb=" CA PRO F 40 " pdb=" N PRO F 40 " pdb=" CD PRO F 40 " ideal model delta sigma weight residual 112.00 95.54 16.46 1.40e+00 5.10e-01 1.38e+02 angle pdb=" N PRO F 40 " pdb=" CD PRO F 40 " pdb=" CG PRO F 40 " ideal model delta sigma weight residual 103.20 87.93 15.27 1.50e+00 4.44e-01 1.04e+02 angle pdb=" CA GLY C 447 " pdb=" C GLY C 447 " pdb=" O GLY C 447 " ideal model delta sigma weight residual 121.88 114.92 6.96 7.80e-01 1.64e+00 7.97e+01 angle pdb=" N PRO G 59 " pdb=" CD PRO G 59 " pdb=" CG PRO G 59 " ideal model delta sigma weight residual 103.20 90.02 13.18 1.50e+00 4.44e-01 7.72e+01 angle pdb=" C PHE A 140 " pdb=" CA PHE A 140 " pdb=" CB PHE A 140 " ideal model delta sigma weight residual 111.17 95.96 15.21 1.96e+00 2.60e-01 6.02e+01 ... (remaining 44809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.66: 19383 21.66 - 43.32: 1006 43.32 - 64.98: 116 64.98 - 86.64: 45 86.64 - 108.30: 15 Dihedral angle restraints: 20565 sinusoidal: 8949 harmonic: 11616 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.51 -80.49 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -9.81 -76.19 1 1.00e+01 1.00e-02 7.31e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -10.44 -75.56 1 1.00e+01 1.00e-02 7.21e+01 ... (remaining 20562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4792 0.096 - 0.192: 416 0.192 - 0.288: 44 0.288 - 0.384: 3 0.384 - 0.479: 4 Chirality restraints: 5259 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.33e+01 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.10e+01 ... (remaining 5256 not shown) Planarity restraints: 5751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " -0.244 2.00e-02 2.50e+03 2.07e-01 5.37e+02 pdb=" C7 NAG I 2 " 0.051 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " 0.342 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.232 2.00e-02 2.50e+03 1.97e-01 4.86e+02 pdb=" C7 NAG K 2 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.323 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 2 " -0.221 2.00e-02 2.50e+03 1.88e-01 4.42e+02 pdb=" C7 NAG P 2 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG P 2 " 0.038 2.00e-02 2.50e+03 pdb=" N2 NAG P 2 " 0.308 2.00e-02 2.50e+03 pdb=" O7 NAG P 2 " -0.171 2.00e-02 2.50e+03 ... (remaining 5748 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5085 2.77 - 3.30: 28806 3.30 - 3.83: 52493 3.83 - 4.37: 59924 4.37 - 4.90: 106489 Nonbonded interactions: 252797 Sorted by model distance: nonbonded pdb=" OG SER B 494 " pdb=" OH TYR F 32 " model vdw 2.232 3.040 nonbonded pdb=" OE1 GLN B 314 " pdb=" OG SER C 735 " model vdw 2.282 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 21 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.315 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.331 3.040 ... (remaining 252792 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 31.640 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 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 : 0.005 0.259 33075 Z= 0.288 Angle : 0.900 16.459 45147 Z= 0.521 Chirality : 0.057 0.479 5259 Planarity : 0.008 0.207 5700 Dihedral : 12.843 108.299 12957 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 3.17 % 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: -0.75 (0.12), residues: 3954 helix: -0.05 (0.18), residues: 741 sheet: 0.48 (0.17), residues: 963 loop : -1.11 (0.12), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 61 TYR 0.035 0.002 TYR B 741 PHE 0.043 0.002 PHE C 817 TRP 0.034 0.002 TRP G 35 HIS 0.012 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00543 (32946) covalent geometry : angle 0.88817 (44814) SS BOND : bond 0.00599 ( 54) SS BOND : angle 1.48435 ( 108) hydrogen bonds : bond 0.21728 ( 1235) hydrogen bonds : angle 8.67611 ( 3528) link_BETA1-4 : bond 0.00589 ( 24) link_BETA1-4 : angle 1.74236 ( 72) link_NAG-ASN : bond 0.00610 ( 51) link_NAG-ASN : angle 2.18990 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 1.194 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: A 725 GLU cc_start: 0.7602 (pp20) cc_final: 0.7284 (pp20) REVERT: A 864 LEU cc_start: 0.7503 (tp) cc_final: 0.7118 (tp) REVERT: H 4 LEU cc_start: 0.8613 (mm) cc_final: 0.8249 (mm) REVERT: H 57 THR cc_start: 0.8853 (p) cc_final: 0.8553 (m) REVERT: L 53 SER cc_start: 0.7978 (t) cc_final: 0.7589 (p) REVERT: B 406 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6757 (mm-30) REVERT: D 4 LEU cc_start: 0.8327 (mm) cc_final: 0.7838 (mm) REVERT: F 2 ILE cc_start: 0.8291 (mp) cc_final: 0.8029 (mp) REVERT: F 27 GLN cc_start: 0.7368 (pt0) cc_final: 0.6528 (pp30) REVERT: F 53 SER cc_start: 0.8263 (t) cc_final: 0.7733 (p) REVERT: F 54 ARG cc_start: 0.7958 (mpt90) cc_final: 0.7534 (mtt90) REVERT: E 4 LEU cc_start: 0.8408 (mm) cc_final: 0.8158 (mm) REVERT: E 101 ASP cc_start: 0.8075 (t0) cc_final: 0.7805 (t0) REVERT: G 49 TYR cc_start: 0.8182 (p90) cc_final: 0.7798 (p90) REVERT: G 53 SER cc_start: 0.7441 (t) cc_final: 0.7026 (t) REVERT: G 79 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7176 (pm20) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.2077 time to fit residues: 147.2100 Evaluate side-chains 312 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 498 GLN A 519 HIS A 613 GLN A 644 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 498 GLN B 519 HIS B 613 GLN B 644 GLN B1011 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 519 HIS ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.128820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.100208 restraints weight = 67125.556| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.12 r_work: 0.3514 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33075 Z= 0.158 Angle : 0.608 10.448 45147 Z= 0.312 Chirality : 0.044 0.199 5259 Planarity : 0.004 0.062 5700 Dihedral : 6.364 66.255 5895 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.81 % Allowed : 7.47 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 (0.13), residues: 3954 helix: 0.83 (0.19), residues: 744 sheet: 0.50 (0.16), residues: 1056 loop : -0.89 (0.12), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 18 TYR 0.022 0.001 TYR B1067 PHE 0.021 0.001 PHE A 140 TRP 0.018 0.001 TRP F 35 HIS 0.004 0.001 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00357 (32946) covalent geometry : angle 0.59906 (44814) SS BOND : bond 0.00342 ( 54) SS BOND : angle 1.02439 ( 108) hydrogen bonds : bond 0.04796 ( 1235) hydrogen bonds : angle 6.33161 ( 3528) link_BETA1-4 : bond 0.00258 ( 24) link_BETA1-4 : angle 1.64297 ( 72) link_NAG-ASN : bond 0.00295 ( 51) link_NAG-ASN : angle 1.39254 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 341 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.7190 (p0) cc_final: 0.6915 (p0) REVERT: A 1005 GLN cc_start: 0.7613 (tm-30) cc_final: 0.7366 (tm-30) REVERT: H 107 THR cc_start: 0.7806 (p) cc_final: 0.7500 (t) REVERT: L 77 ARG cc_start: 0.8651 (ttp80) cc_final: 0.8373 (ttp80) REVERT: B 131 CYS cc_start: 0.6642 (m) cc_final: 0.6378 (m) REVERT: B 869 MET cc_start: 0.8699 (mtm) cc_final: 0.8449 (ttm) REVERT: D 58 GLU cc_start: 0.8089 (mp0) cc_final: 0.7802 (mp0) REVERT: F 2 ILE cc_start: 0.8533 (mp) cc_final: 0.8115 (mp) REVERT: F 27 GLN cc_start: 0.8257 (pt0) cc_final: 0.7532 (pp30) REVERT: F 53 SER cc_start: 0.7740 (t) cc_final: 0.7379 (p) REVERT: F 62 PHE cc_start: 0.6821 (m-80) cc_final: 0.6611 (m-80) REVERT: F 77 ARG cc_start: 0.8660 (ttp-110) cc_final: 0.8394 (ttp-110) REVERT: C 389 ASP cc_start: 0.6423 (p0) cc_final: 0.5992 (p0) REVERT: C 390 LEU cc_start: 0.7520 (mt) cc_final: 0.7297 (mt) REVERT: C 740 MET cc_start: 0.8792 (mmm) cc_final: 0.8484 (tpt) REVERT: C 1005 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7474 (tm-30) REVERT: E 81 GLN cc_start: 0.8136 (tp40) cc_final: 0.7930 (tp40) REVERT: E 101 ASP cc_start: 0.8318 (t0) cc_final: 0.8002 (t0) REVERT: E 105 GLN cc_start: 0.8621 (mp10) cc_final: 0.8339 (mp10) REVERT: G 77 ARG cc_start: 0.8320 (ttp-110) cc_final: 0.8078 (ttp-110) outliers start: 28 outliers final: 20 residues processed: 360 average time/residue: 0.2077 time to fit residues: 118.0910 Evaluate side-chains 317 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 297 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 256 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 207 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 343 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 935 GLN A1064 HIS ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 519 HIS C 613 GLN C 901 GLN G 37 GLN ** G 100 GLN ** 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 = 0.4022 r_free = 0.4022 target = 0.122281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.092272 restraints weight = 68959.557| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.44 r_work: 0.3433 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 33075 Z= 0.154 Angle : 0.570 8.887 45147 Z= 0.291 Chirality : 0.043 0.167 5259 Planarity : 0.004 0.042 5700 Dihedral : 4.975 35.698 5895 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.30 % Allowed : 9.47 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.16 (0.13), residues: 3954 helix: 1.09 (0.20), residues: 726 sheet: 0.55 (0.16), residues: 1017 loop : -0.84 (0.12), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 45 TYR 0.021 0.001 TYR B1067 PHE 0.014 0.001 PHE C 347 TRP 0.024 0.001 TRP F 35 HIS 0.004 0.001 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00353 (32946) covalent geometry : angle 0.56151 (44814) SS BOND : bond 0.00294 ( 54) SS BOND : angle 1.04483 ( 108) hydrogen bonds : bond 0.04354 ( 1235) hydrogen bonds : angle 5.77339 ( 3528) link_BETA1-4 : bond 0.00329 ( 24) link_BETA1-4 : angle 1.50201 ( 72) link_NAG-ASN : bond 0.00248 ( 51) link_NAG-ASN : angle 1.29129 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 325 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.7153 (p0) cc_final: 0.6865 (p0) REVERT: A 740 MET cc_start: 0.8967 (mtp) cc_final: 0.8663 (tpp) REVERT: H 101 ASP cc_start: 0.8285 (t0) cc_final: 0.7987 (t0) REVERT: H 107 THR cc_start: 0.7917 (p) cc_final: 0.7644 (t) REVERT: L 27 GLN cc_start: 0.7997 (pp30) cc_final: 0.7558 (pp30) REVERT: L 77 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8580 (ttp80) REVERT: L 103 LYS cc_start: 0.8247 (tppt) cc_final: 0.7866 (tppt) REVERT: B 131 CYS cc_start: 0.6782 (m) cc_final: 0.6444 (m) REVERT: B 389 ASP cc_start: 0.6413 (p0) cc_final: 0.6043 (p0) REVERT: B 740 MET cc_start: 0.8827 (tpt) cc_final: 0.8581 (tpp) REVERT: B 900 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7942 (mtm) REVERT: B 1005 GLN cc_start: 0.8313 (tt0) cc_final: 0.7905 (tm-30) REVERT: B 1012 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5978 (tp) REVERT: B 1029 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8146 (tpp) REVERT: B 1138 TYR cc_start: 0.7565 (t80) cc_final: 0.7290 (m-10) REVERT: D 97 ARG cc_start: 0.8837 (ttt-90) cc_final: 0.8567 (ttt-90) REVERT: F 2 ILE cc_start: 0.8585 (mp) cc_final: 0.8173 (mp) REVERT: F 27 GLN cc_start: 0.8247 (pt0) cc_final: 0.7600 (pp30) REVERT: F 53 SER cc_start: 0.7569 (t) cc_final: 0.7160 (t) REVERT: F 54 ARG cc_start: 0.8120 (mtt90) cc_final: 0.7116 (mtt90) REVERT: F 77 ARG cc_start: 0.8737 (ttp-110) cc_final: 0.8425 (ttp-110) REVERT: C 131 CYS cc_start: 0.7123 (m) cc_final: 0.6849 (m) REVERT: C 389 ASP cc_start: 0.6363 (p0) cc_final: 0.5909 (p0) REVERT: C 390 LEU cc_start: 0.7732 (mt) cc_final: 0.7441 (mt) REVERT: C 406 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8107 (mm-30) REVERT: C 740 MET cc_start: 0.8716 (mmm) cc_final: 0.8392 (tpt) REVERT: C 965 GLN cc_start: 0.8101 (tp40) cc_final: 0.7550 (mm110) REVERT: C 1005 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7378 (tm-30) REVERT: E 101 ASP cc_start: 0.8480 (t0) cc_final: 0.8019 (t0) REVERT: E 105 GLN cc_start: 0.8738 (mp10) cc_final: 0.8495 (mp10) REVERT: G 77 ARG cc_start: 0.8586 (ttp-110) cc_final: 0.8252 (ttp-110) outliers start: 45 outliers final: 30 residues processed: 355 average time/residue: 0.1995 time to fit residues: 114.0614 Evaluate side-chains 324 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 291 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 9 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 351 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 265 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 935 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 564 GLN B 804 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 519 HIS ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN G 42 GLN ** G 100 GLN ** 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 = 0.4015 r_free = 0.4015 target = 0.120826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.091458 restraints weight = 67162.547| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.17 r_work: 0.3392 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 33075 Z= 0.203 Angle : 0.606 10.354 45147 Z= 0.309 Chirality : 0.044 0.175 5259 Planarity : 0.004 0.048 5700 Dihedral : 4.651 35.327 5895 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.20 % Allowed : 10.83 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.11 (0.13), residues: 3954 helix: 1.00 (0.19), residues: 762 sheet: 0.65 (0.16), residues: 963 loop : -0.79 (0.12), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 45 TYR 0.020 0.002 TYR B1067 PHE 0.024 0.002 PHE C 347 TRP 0.031 0.002 TRP F 35 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00470 (32946) covalent geometry : angle 0.59701 (44814) SS BOND : bond 0.00330 ( 54) SS BOND : angle 1.18092 ( 108) hydrogen bonds : bond 0.04422 ( 1235) hydrogen bonds : angle 5.64448 ( 3528) link_BETA1-4 : bond 0.00459 ( 24) link_BETA1-4 : angle 1.39635 ( 72) link_NAG-ASN : bond 0.00299 ( 51) link_NAG-ASN : angle 1.38387 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 308 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.7215 (p0) cc_final: 0.6886 (p0) REVERT: A 740 MET cc_start: 0.8992 (mtp) cc_final: 0.8709 (tpp) REVERT: H 59 TYR cc_start: 0.8830 (m-80) cc_final: 0.8619 (m-80) REVERT: H 67 PHE cc_start: 0.7466 (m-10) cc_final: 0.7260 (m-80) REVERT: H 101 ASP cc_start: 0.8291 (t0) cc_final: 0.7933 (t0) REVERT: H 107 THR cc_start: 0.7810 (p) cc_final: 0.7582 (t) REVERT: L 27 GLN cc_start: 0.8017 (pp30) cc_final: 0.7553 (pp30) REVERT: L 77 ARG cc_start: 0.8890 (ttp80) cc_final: 0.8676 (ttp-110) REVERT: B 131 CYS cc_start: 0.6793 (m) cc_final: 0.6442 (m) REVERT: B 495 TYR cc_start: 0.8730 (m-10) cc_final: 0.8358 (m-10) REVERT: B 740 MET cc_start: 0.8834 (tpt) cc_final: 0.8563 (tpp) REVERT: B 900 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8103 (mtm) REVERT: B 1005 GLN cc_start: 0.8276 (tt0) cc_final: 0.7946 (tm-30) REVERT: B 1029 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8259 (tpp) REVERT: B 1138 TYR cc_start: 0.7716 (t80) cc_final: 0.7413 (m-10) REVERT: D 102 TYR cc_start: 0.7785 (t80) cc_final: 0.7488 (t80) REVERT: F 2 ILE cc_start: 0.8653 (mp) cc_final: 0.8259 (mp) REVERT: F 27 GLN cc_start: 0.8305 (pt0) cc_final: 0.7604 (pp30) REVERT: F 42 GLN cc_start: 0.8321 (mm110) cc_final: 0.7969 (tm-30) REVERT: F 53 SER cc_start: 0.7548 (t) cc_final: 0.7112 (t) REVERT: F 54 ARG cc_start: 0.8175 (mtt90) cc_final: 0.7165 (mtt90) REVERT: F 77 ARG cc_start: 0.8791 (ttp-110) cc_final: 0.8458 (ttp-110) REVERT: C 131 CYS cc_start: 0.6945 (m) cc_final: 0.6669 (m) REVERT: C 389 ASP cc_start: 0.6539 (p0) cc_final: 0.6022 (p0) REVERT: C 390 LEU cc_start: 0.7853 (mt) cc_final: 0.7486 (mt) REVERT: C 740 MET cc_start: 0.8789 (mmm) cc_final: 0.8389 (tpt) REVERT: C 965 GLN cc_start: 0.8086 (tp40) cc_final: 0.7483 (mm110) REVERT: C 1005 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7586 (tm-30) REVERT: C 1138 TYR cc_start: 0.7973 (t80) cc_final: 0.7645 (m-10) REVERT: E 101 ASP cc_start: 0.8536 (t0) cc_final: 0.8014 (t0) REVERT: E 105 GLN cc_start: 0.8757 (mp10) cc_final: 0.8552 (mp10) REVERT: G 48 ILE cc_start: 0.8014 (mt) cc_final: 0.7586 (mm) outliers start: 76 outliers final: 54 residues processed: 363 average time/residue: 0.1983 time to fit residues: 116.4267 Evaluate side-chains 340 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 284 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 164 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 193 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 338 optimal weight: 2.9990 chunk 308 optimal weight: 0.0370 chunk 242 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 115 optimal weight: 0.0970 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.130335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.099151 restraints weight = 72279.936| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.09 r_work: 0.3471 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 33075 Z= 0.107 Angle : 0.532 7.963 45147 Z= 0.272 Chirality : 0.042 0.160 5259 Planarity : 0.003 0.044 5700 Dihedral : 4.297 32.038 5895 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.59 % Allowed : 12.57 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.04 (0.13), residues: 3954 helix: 1.31 (0.20), residues: 762 sheet: 0.53 (0.16), residues: 1023 loop : -0.79 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 45 TYR 0.021 0.001 TYR B1067 PHE 0.018 0.001 PHE A 133 TRP 0.029 0.001 TRP F 35 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00239 (32946) covalent geometry : angle 0.52454 (44814) SS BOND : bond 0.00389 ( 54) SS BOND : angle 1.03136 ( 108) hydrogen bonds : bond 0.03765 ( 1235) hydrogen bonds : angle 5.33586 ( 3528) link_BETA1-4 : bond 0.00358 ( 24) link_BETA1-4 : angle 1.18883 ( 72) link_NAG-ASN : bond 0.00192 ( 51) link_NAG-ASN : angle 1.19213 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 330 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.7068 (p0) cc_final: 0.6717 (p0) REVERT: A 740 MET cc_start: 0.8900 (mtp) cc_final: 0.8646 (tpp) REVERT: A 1092 GLU cc_start: 0.7362 (pp20) cc_final: 0.7161 (pp20) REVERT: H 59 TYR cc_start: 0.8868 (m-80) cc_final: 0.8617 (m-80) REVERT: H 67 PHE cc_start: 0.7282 (m-10) cc_final: 0.7024 (m-80) REVERT: H 97 ARG cc_start: 0.8684 (ttt-90) cc_final: 0.7681 (tmt-80) REVERT: H 101 ASP cc_start: 0.8251 (t0) cc_final: 0.7862 (t0) REVERT: L 27 GLN cc_start: 0.7977 (pp30) cc_final: 0.7512 (pp30) REVERT: B 131 CYS cc_start: 0.6509 (m) cc_final: 0.6207 (m) REVERT: B 740 MET cc_start: 0.8699 (tpt) cc_final: 0.8483 (tpp) REVERT: B 900 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7773 (mtm) REVERT: B 1029 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8109 (tpp) REVERT: D 102 TYR cc_start: 0.7779 (t80) cc_final: 0.7441 (t80) REVERT: F 2 ILE cc_start: 0.8588 (mp) cc_final: 0.8157 (mp) REVERT: F 27 GLN cc_start: 0.8289 (pt0) cc_final: 0.7698 (pp30) REVERT: F 48 ILE cc_start: 0.8114 (mt) cc_final: 0.7715 (mm) REVERT: F 54 ARG cc_start: 0.8049 (mtt90) cc_final: 0.7330 (mtt90) REVERT: F 62 PHE cc_start: 0.7918 (m-80) cc_final: 0.7397 (m-80) REVERT: F 77 ARG cc_start: 0.8778 (ttp-110) cc_final: 0.8572 (ttp-110) REVERT: C 131 CYS cc_start: 0.6771 (m) cc_final: 0.6528 (m) REVERT: C 389 ASP cc_start: 0.6431 (p0) cc_final: 0.5936 (p0) REVERT: C 390 LEU cc_start: 0.7570 (mt) cc_final: 0.7153 (mt) REVERT: C 740 MET cc_start: 0.8662 (mmm) cc_final: 0.8333 (tpt) REVERT: C 902 MET cc_start: 0.8780 (mmt) cc_final: 0.8558 (mmt) REVERT: C 965 GLN cc_start: 0.7918 (tp40) cc_final: 0.7425 (mm110) REVERT: C 1138 TYR cc_start: 0.7989 (t80) cc_final: 0.7685 (m-10) REVERT: E 82 MET cc_start: 0.7268 (mmm) cc_final: 0.7042 (mmp) REVERT: E 101 ASP cc_start: 0.8404 (t0) cc_final: 0.7845 (t0) REVERT: G 48 ILE cc_start: 0.7997 (mt) cc_final: 0.7741 (mm) outliers start: 55 outliers final: 41 residues processed: 368 average time/residue: 0.2056 time to fit residues: 121.1543 Evaluate side-chains 342 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 299 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 125 optimal weight: 0.6980 chunk 208 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 314 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.120208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.090533 restraints weight = 67294.487| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.28 r_work: 0.3404 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33075 Z= 0.149 Angle : 0.558 10.018 45147 Z= 0.284 Chirality : 0.043 0.167 5259 Planarity : 0.004 0.044 5700 Dihedral : 4.263 33.403 5895 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.94 % Allowed : 13.70 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 0.05 (0.13), residues: 3954 helix: 1.34 (0.20), residues: 744 sheet: 0.73 (0.16), residues: 951 loop : -0.73 (0.12), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 214 TYR 0.022 0.001 TYR L 87 PHE 0.015 0.001 PHE B 347 TRP 0.031 0.001 TRP F 35 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00346 (32946) covalent geometry : angle 0.55022 (44814) SS BOND : bond 0.00290 ( 54) SS BOND : angle 1.07114 ( 108) hydrogen bonds : bond 0.03902 ( 1235) hydrogen bonds : angle 5.31552 ( 3528) link_BETA1-4 : bond 0.00291 ( 24) link_BETA1-4 : angle 1.19731 ( 72) link_NAG-ASN : bond 0.00216 ( 51) link_NAG-ASN : angle 1.25646 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 299 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9009 (mtp) cc_final: 0.8706 (tpp) REVERT: A 1092 GLU cc_start: 0.7545 (pp20) cc_final: 0.7274 (pp20) REVERT: H 59 TYR cc_start: 0.8842 (m-80) cc_final: 0.8568 (m-80) REVERT: H 67 PHE cc_start: 0.6882 (m-10) cc_final: 0.6667 (m-80) REVERT: H 97 ARG cc_start: 0.8815 (ttt-90) cc_final: 0.7712 (tmt-80) REVERT: H 101 ASP cc_start: 0.8324 (t0) cc_final: 0.7877 (t0) REVERT: L 27 GLN cc_start: 0.7964 (pp30) cc_final: 0.7417 (pp30) REVERT: L 39 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7850 (mtmm) REVERT: L 62 PHE cc_start: 0.8236 (m-80) cc_final: 0.7789 (m-80) REVERT: B 131 CYS cc_start: 0.6718 (m) cc_final: 0.6347 (m) REVERT: B 495 TYR cc_start: 0.8787 (m-10) cc_final: 0.8272 (m-10) REVERT: B 740 MET cc_start: 0.8817 (tpt) cc_final: 0.8557 (tpp) REVERT: B 900 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.7993 (mtm) REVERT: B 1005 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7561 (tm-30) REVERT: B 1029 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8208 (tpp) REVERT: D 102 TYR cc_start: 0.7816 (t80) cc_final: 0.7470 (t80) REVERT: F 2 ILE cc_start: 0.8600 (mp) cc_final: 0.8262 (mp) REVERT: F 27 GLN cc_start: 0.8281 (pt0) cc_final: 0.7614 (pp30) REVERT: F 48 ILE cc_start: 0.8453 (mt) cc_final: 0.8174 (mm) REVERT: F 54 ARG cc_start: 0.8156 (mtt90) cc_final: 0.7789 (mtt90) REVERT: F 81 GLU cc_start: 0.6759 (pm20) cc_final: 0.6551 (pm20) REVERT: C 131 CYS cc_start: 0.6806 (m) cc_final: 0.6529 (m) REVERT: C 389 ASP cc_start: 0.6560 (p0) cc_final: 0.6032 (p0) REVERT: C 390 LEU cc_start: 0.7798 (mt) cc_final: 0.7345 (mt) REVERT: C 740 MET cc_start: 0.8829 (mmm) cc_final: 0.8461 (tpt) REVERT: C 1138 TYR cc_start: 0.8081 (t80) cc_final: 0.7640 (m-10) REVERT: E 101 ASP cc_start: 0.8455 (t0) cc_final: 0.7852 (t0) REVERT: E 105 GLN cc_start: 0.8877 (mp10) cc_final: 0.8649 (mp10) REVERT: G 48 ILE cc_start: 0.8110 (mt) cc_final: 0.7747 (mm) REVERT: G 77 ARG cc_start: 0.8598 (ttp-110) cc_final: 0.8230 (ttp-110) REVERT: G 103 LYS cc_start: 0.8453 (tptt) cc_final: 0.8124 (tptp) outliers start: 67 outliers final: 53 residues processed: 347 average time/residue: 0.2035 time to fit residues: 113.7062 Evaluate side-chains 344 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 289 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 80 optimal weight: 8.9990 chunk 236 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 chunk 358 optimal weight: 3.9990 chunk 42 optimal weight: 0.0070 chunk 81 optimal weight: 1.9990 chunk 298 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 229 optimal weight: 0.5980 chunk 202 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 519 HIS C 856 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.130052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.098413 restraints weight = 71693.980| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.08 r_work: 0.3450 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33075 Z= 0.112 Angle : 0.534 8.636 45147 Z= 0.272 Chirality : 0.042 0.160 5259 Planarity : 0.003 0.042 5700 Dihedral : 4.110 31.382 5895 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.80 % Allowed : 14.34 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 (0.13), residues: 3954 helix: 1.33 (0.20), residues: 765 sheet: 0.50 (0.16), residues: 1053 loop : -0.65 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 45 TYR 0.021 0.001 TYR L 87 PHE 0.013 0.001 PHE H 67 TRP 0.036 0.001 TRP F 35 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00257 (32946) covalent geometry : angle 0.52770 (44814) SS BOND : bond 0.00253 ( 54) SS BOND : angle 0.96349 ( 108) hydrogen bonds : bond 0.03618 ( 1235) hydrogen bonds : angle 5.16259 ( 3528) link_BETA1-4 : bond 0.00346 ( 24) link_BETA1-4 : angle 1.13912 ( 72) link_NAG-ASN : bond 0.00183 ( 51) link_NAG-ASN : angle 1.16020 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 303 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8902 (mtp) cc_final: 0.8650 (tpp) REVERT: A 1092 GLU cc_start: 0.7412 (pp20) cc_final: 0.7173 (pp20) REVERT: H 59 TYR cc_start: 0.8863 (m-80) cc_final: 0.8637 (m-80) REVERT: H 97 ARG cc_start: 0.8681 (ttt-90) cc_final: 0.7780 (tmt-80) REVERT: H 101 ASP cc_start: 0.8284 (t0) cc_final: 0.7843 (t0) REVERT: L 27 GLN cc_start: 0.8009 (pp30) cc_final: 0.7498 (pp30) REVERT: L 42 GLN cc_start: 0.8147 (pm20) cc_final: 0.7631 (pp30) REVERT: B 131 CYS cc_start: 0.6560 (m) cc_final: 0.6226 (m) REVERT: B 740 MET cc_start: 0.8681 (tpt) cc_final: 0.8459 (tpp) REVERT: B 900 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7791 (mtm) REVERT: B 1029 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8082 (tpp) REVERT: D 82 MET cc_start: 0.6980 (mmm) cc_final: 0.6754 (mmm) REVERT: D 102 TYR cc_start: 0.7734 (t80) cc_final: 0.7377 (t80) REVERT: F 2 ILE cc_start: 0.8532 (mp) cc_final: 0.8189 (mp) REVERT: F 27 GLN cc_start: 0.8279 (pt0) cc_final: 0.7698 (pp30) REVERT: F 48 ILE cc_start: 0.8322 (mt) cc_final: 0.8089 (mm) REVERT: F 54 ARG cc_start: 0.8111 (mtt90) cc_final: 0.7844 (mtt90) REVERT: C 131 CYS cc_start: 0.6667 (m) cc_final: 0.6417 (m) REVERT: C 389 ASP cc_start: 0.6509 (p0) cc_final: 0.6029 (p0) REVERT: C 740 MET cc_start: 0.8751 (mmm) cc_final: 0.8448 (tpt) REVERT: C 1138 TYR cc_start: 0.7979 (t80) cc_final: 0.7692 (m-10) REVERT: E 58 GLU cc_start: 0.8314 (mp0) cc_final: 0.8074 (mp0) REVERT: E 101 ASP cc_start: 0.8439 (t0) cc_final: 0.7914 (t0) REVERT: E 105 GLN cc_start: 0.8877 (mp10) cc_final: 0.8649 (mp10) REVERT: G 27 GLN cc_start: 0.8053 (pp30) cc_final: 0.7783 (pp30) REVERT: G 48 ILE cc_start: 0.8063 (mt) cc_final: 0.7851 (mm) REVERT: G 103 LYS cc_start: 0.8323 (tptt) cc_final: 0.8052 (tptt) outliers start: 62 outliers final: 50 residues processed: 347 average time/residue: 0.2024 time to fit residues: 113.1112 Evaluate side-chains 344 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 292 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 376 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 323 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 356 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 352 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A 978 ASN A1005 GLN A1135 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 207 HIS C1002 GLN C1135 ASN ** G 100 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 = 0.3973 r_free = 0.3973 target = 0.125405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.093409 restraints weight = 71291.478| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.99 r_work: 0.3367 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 33075 Z= 0.269 Angle : 0.655 10.671 45147 Z= 0.331 Chirality : 0.045 0.185 5259 Planarity : 0.004 0.047 5700 Dihedral : 4.583 37.106 5895 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.29 % Allowed : 14.28 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.15 (0.13), residues: 3954 helix: 0.90 (0.19), residues: 762 sheet: 0.44 (0.16), residues: 1047 loop : -0.73 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 77 TYR 0.022 0.002 TYR H 79 PHE 0.025 0.002 PHE B 347 TRP 0.033 0.002 TRP F 35 HIS 0.008 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00630 (32946) covalent geometry : angle 0.64661 (44814) SS BOND : bond 0.00394 ( 54) SS BOND : angle 1.24410 ( 108) hydrogen bonds : bond 0.04563 ( 1235) hydrogen bonds : angle 5.48542 ( 3528) link_BETA1-4 : bond 0.00245 ( 24) link_BETA1-4 : angle 1.26106 ( 72) link_NAG-ASN : bond 0.00326 ( 51) link_NAG-ASN : angle 1.49665 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 285 time to evaluate : 1.088 Fit side-chains REVERT: A 740 MET cc_start: 0.8960 (mtp) cc_final: 0.8686 (tpp) REVERT: A 789 TYR cc_start: 0.8494 (m-80) cc_final: 0.8214 (m-80) REVERT: A 1092 GLU cc_start: 0.7596 (pp20) cc_final: 0.7352 (pp20) REVERT: H 59 TYR cc_start: 0.8948 (m-80) cc_final: 0.8683 (m-80) REVERT: H 97 ARG cc_start: 0.8776 (ttt-90) cc_final: 0.7797 (tmt-80) REVERT: H 101 ASP cc_start: 0.8220 (t0) cc_final: 0.7957 (t0) REVERT: L 27 GLN cc_start: 0.7985 (pp30) cc_final: 0.7468 (pp30) REVERT: L 54 ARG cc_start: 0.8322 (mtt90) cc_final: 0.7617 (mtt90) REVERT: L 62 PHE cc_start: 0.8328 (m-80) cc_final: 0.7811 (m-80) REVERT: B 131 CYS cc_start: 0.6762 (m) cc_final: 0.6512 (m) REVERT: B 313 TYR cc_start: 0.8204 (m-80) cc_final: 0.7907 (m-80) REVERT: B 740 MET cc_start: 0.8798 (tpt) cc_final: 0.8597 (mmm) REVERT: B 900 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8137 (mtm) REVERT: B 1029 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8287 (tpp) REVERT: D 102 TYR cc_start: 0.7803 (t80) cc_final: 0.7458 (t80) REVERT: F 27 GLN cc_start: 0.8370 (pt0) cc_final: 0.7764 (pp30) REVERT: F 42 GLN cc_start: 0.8259 (mm-40) cc_final: 0.8000 (tm-30) REVERT: C 131 CYS cc_start: 0.6765 (m) cc_final: 0.6505 (m) REVERT: C 389 ASP cc_start: 0.6906 (p0) cc_final: 0.6129 (p0) REVERT: C 390 LEU cc_start: 0.8066 (mt) cc_final: 0.7540 (mt) REVERT: C 467 ASP cc_start: 0.8500 (p0) cc_final: 0.8175 (p0) REVERT: C 740 MET cc_start: 0.8823 (mmm) cc_final: 0.8376 (tmm) REVERT: C 1138 TYR cc_start: 0.8038 (t80) cc_final: 0.7826 (m-10) REVERT: E 58 GLU cc_start: 0.8218 (mp0) cc_final: 0.8003 (mp0) REVERT: E 101 ASP cc_start: 0.8366 (t0) cc_final: 0.8125 (t0) REVERT: E 105 GLN cc_start: 0.8872 (mp10) cc_final: 0.8478 (mp10) REVERT: G 27 GLN cc_start: 0.8027 (pp30) cc_final: 0.7508 (pp30) REVERT: G 48 ILE cc_start: 0.8091 (mt) cc_final: 0.7790 (mm) REVERT: G 103 LYS cc_start: 0.8192 (tptt) cc_final: 0.7932 (tptt) outliers start: 79 outliers final: 65 residues processed: 340 average time/residue: 0.2017 time to fit residues: 109.2111 Evaluate side-chains 344 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 277 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 328 optimal weight: 0.9990 chunk 386 optimal weight: 3.9990 chunk 236 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 384 optimal weight: 8.9990 chunk 231 optimal weight: 0.8980 chunk 299 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 519 HIS C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.127661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.095914 restraints weight = 70624.634| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.00 r_work: 0.3419 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33075 Z= 0.139 Angle : 0.568 8.835 45147 Z= 0.289 Chirality : 0.043 0.169 5259 Planarity : 0.004 0.045 5700 Dihedral : 4.415 34.124 5895 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.85 % Allowed : 14.83 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 (0.13), residues: 3954 helix: 1.15 (0.19), residues: 765 sheet: 0.58 (0.16), residues: 1005 loop : -0.71 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 45 TYR 0.020 0.001 TYR B1067 PHE 0.013 0.001 PHE C 347 TRP 0.026 0.001 TRP F 35 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00322 (32946) covalent geometry : angle 0.55870 (44814) SS BOND : bond 0.00401 ( 54) SS BOND : angle 1.39260 ( 108) hydrogen bonds : bond 0.03913 ( 1235) hydrogen bonds : angle 5.24716 ( 3528) link_BETA1-4 : bond 0.00351 ( 24) link_BETA1-4 : angle 1.12905 ( 72) link_NAG-ASN : bond 0.00274 ( 51) link_NAG-ASN : angle 1.31151 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 287 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 740 MET cc_start: 0.8934 (mtp) cc_final: 0.8628 (tpp) REVERT: A 1092 GLU cc_start: 0.7500 (pp20) cc_final: 0.7298 (pp20) REVERT: H 52 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8008 (mppt) REVERT: H 58 GLU cc_start: 0.7921 (mp0) cc_final: 0.7600 (tt0) REVERT: H 59 TYR cc_start: 0.8937 (m-80) cc_final: 0.8552 (m-80) REVERT: H 101 ASP cc_start: 0.8285 (t0) cc_final: 0.7817 (t0) REVERT: L 24 ARG cc_start: 0.8608 (tpp80) cc_final: 0.7326 (tpp80) REVERT: L 27 GLN cc_start: 0.7981 (pp30) cc_final: 0.7391 (pp30) REVERT: L 39 LYS cc_start: 0.8266 (mtmm) cc_final: 0.7722 (pttt) REVERT: B 131 CYS cc_start: 0.6705 (m) cc_final: 0.6470 (m) REVERT: B 313 TYR cc_start: 0.8123 (m-80) cc_final: 0.7889 (m-80) REVERT: B 495 TYR cc_start: 0.8798 (m-10) cc_final: 0.8316 (m-10) REVERT: B 740 MET cc_start: 0.8723 (tpt) cc_final: 0.8522 (mmm) REVERT: B 900 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7925 (mtm) REVERT: B 980 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8139 (tt) REVERT: B 1029 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8189 (tpp) REVERT: D 82 MET cc_start: 0.7277 (mmm) cc_final: 0.7038 (mmm) REVERT: D 102 TYR cc_start: 0.7757 (t80) cc_final: 0.7417 (t80) REVERT: F 27 GLN cc_start: 0.8353 (pt0) cc_final: 0.7827 (pp30) REVERT: F 42 GLN cc_start: 0.8263 (mm110) cc_final: 0.8015 (tm-30) REVERT: C 131 CYS cc_start: 0.6711 (m) cc_final: 0.6438 (m) REVERT: C 389 ASP cc_start: 0.6780 (p0) cc_final: 0.6199 (p0) REVERT: C 390 LEU cc_start: 0.7875 (mt) cc_final: 0.7422 (mt) REVERT: C 740 MET cc_start: 0.8778 (mmm) cc_final: 0.8415 (tmm) REVERT: C 965 GLN cc_start: 0.8053 (tp40) cc_final: 0.7801 (tp40) REVERT: E 58 GLU cc_start: 0.8212 (mp0) cc_final: 0.7978 (mp0) REVERT: E 79 TYR cc_start: 0.8494 (m-10) cc_final: 0.8097 (m-10) REVERT: E 101 ASP cc_start: 0.8432 (t0) cc_final: 0.7809 (t0) REVERT: G 48 ILE cc_start: 0.8063 (mt) cc_final: 0.7778 (mm) outliers start: 64 outliers final: 59 residues processed: 333 average time/residue: 0.2026 time to fit residues: 109.1768 Evaluate side-chains 341 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 279 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 62 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 345 optimal weight: 2.9990 chunk 309 optimal weight: 3.9990 chunk 348 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 158 optimal weight: 0.0020 chunk 105 optimal weight: 0.9990 chunk 225 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 207 HIS ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.128614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.096947 restraints weight = 71359.170| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.04 r_work: 0.3433 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33075 Z= 0.121 Angle : 0.554 8.417 45147 Z= 0.282 Chirality : 0.043 0.161 5259 Planarity : 0.004 0.043 5700 Dihedral : 4.242 32.577 5895 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.85 % Allowed : 15.12 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 0.08 (0.13), residues: 3954 helix: 1.27 (0.19), residues: 765 sheet: 0.63 (0.16), residues: 999 loop : -0.66 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 45 TYR 0.020 0.001 TYR B1067 PHE 0.016 0.001 PHE A 133 TRP 0.025 0.001 TRP F 35 HIS 0.003 0.001 HIS E 32 Details of bonding type rmsd covalent geometry : bond 0.00279 (32946) covalent geometry : angle 0.54656 (44814) SS BOND : bond 0.00284 ( 54) SS BOND : angle 1.17263 ( 108) hydrogen bonds : bond 0.03704 ( 1235) hydrogen bonds : angle 5.09996 ( 3528) link_BETA1-4 : bond 0.00328 ( 24) link_BETA1-4 : angle 1.12458 ( 72) link_NAG-ASN : bond 0.00197 ( 51) link_NAG-ASN : angle 1.21395 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 292 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 740 MET cc_start: 0.8857 (mtp) cc_final: 0.8609 (ttm) REVERT: H 52 LYS cc_start: 0.8404 (mmmt) cc_final: 0.8039 (mppt) REVERT: H 58 GLU cc_start: 0.7895 (mp0) cc_final: 0.7602 (tt0) REVERT: H 59 TYR cc_start: 0.8947 (m-80) cc_final: 0.8681 (m-80) REVERT: H 97 ARG cc_start: 0.8683 (ttt-90) cc_final: 0.7753 (tmt-80) REVERT: H 101 ASP cc_start: 0.8257 (t0) cc_final: 0.7796 (t0) REVERT: L 24 ARG cc_start: 0.8604 (tpp80) cc_final: 0.7256 (tpp80) REVERT: L 27 GLN cc_start: 0.7948 (pp30) cc_final: 0.7680 (pp30) REVERT: L 42 GLN cc_start: 0.8217 (pm20) cc_final: 0.7635 (pp30) REVERT: L 77 ARG cc_start: 0.8656 (ttp80) cc_final: 0.8453 (ttp-110) REVERT: B 131 CYS cc_start: 0.6614 (m) cc_final: 0.6379 (m) REVERT: B 313 TYR cc_start: 0.8146 (m-80) cc_final: 0.7920 (m-80) REVERT: B 467 ASP cc_start: 0.8458 (p0) cc_final: 0.8219 (p0) REVERT: B 740 MET cc_start: 0.8748 (tpt) cc_final: 0.8037 (tmm) REVERT: B 900 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7903 (mtm) REVERT: B 1029 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8175 (tpp) REVERT: D 82 MET cc_start: 0.7283 (mmm) cc_final: 0.7066 (mmm) REVERT: D 102 TYR cc_start: 0.7798 (t80) cc_final: 0.7472 (t80) REVERT: F 27 GLN cc_start: 0.8367 (pt0) cc_final: 0.7853 (pp30) REVERT: F 42 GLN cc_start: 0.8256 (mm110) cc_final: 0.7987 (tm-30) REVERT: C 131 CYS cc_start: 0.6681 (m) cc_final: 0.6419 (m) REVERT: C 389 ASP cc_start: 0.6797 (p0) cc_final: 0.6212 (p0) REVERT: C 390 LEU cc_start: 0.7812 (mt) cc_final: 0.7387 (mt) REVERT: C 740 MET cc_start: 0.8781 (mmm) cc_final: 0.8442 (tmm) REVERT: C 965 GLN cc_start: 0.8034 (tp40) cc_final: 0.7800 (tp40) REVERT: E 19 ARG cc_start: 0.7900 (ttm-80) cc_final: 0.7182 (tpt170) REVERT: E 58 GLU cc_start: 0.8224 (mp0) cc_final: 0.7975 (mp0) REVERT: E 79 TYR cc_start: 0.8449 (m-10) cc_final: 0.8027 (m-10) REVERT: E 101 ASP cc_start: 0.8411 (t0) cc_final: 0.7789 (t0) REVERT: G 27 GLN cc_start: 0.7915 (pp30) cc_final: 0.7668 (pp30) REVERT: G 35 TRP cc_start: 0.6885 (m100) cc_final: 0.6422 (m100) REVERT: G 48 ILE cc_start: 0.8089 (mt) cc_final: 0.7799 (mm) REVERT: G 54 ARG cc_start: 0.7715 (mpt180) cc_final: 0.7318 (mpt180) outliers start: 64 outliers final: 59 residues processed: 336 average time/residue: 0.1942 time to fit residues: 105.4599 Evaluate side-chains 344 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 283 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 59 optimal weight: 1.9990 chunk 265 optimal weight: 7.9990 chunk 243 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 369 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 314 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS B 787 GLN ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.128607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.097103 restraints weight = 70589.562| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.90 r_work: 0.3425 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33075 Z= 0.169 Angle : 0.580 10.683 45147 Z= 0.294 Chirality : 0.043 0.166 5259 Planarity : 0.004 0.047 5700 Dihedral : 4.296 33.248 5895 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.91 % Allowed : 15.29 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 0.04 (0.13), residues: 3954 helix: 1.19 (0.19), residues: 765 sheet: 0.62 (0.16), residues: 999 loop : -0.67 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 77 TYR 0.020 0.001 TYR H 79 PHE 0.015 0.001 PHE C 347 TRP 0.022 0.001 TRP F 35 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00395 (32946) covalent geometry : angle 0.57057 (44814) SS BOND : bond 0.00342 ( 54) SS BOND : angle 1.54514 ( 108) hydrogen bonds : bond 0.03860 ( 1235) hydrogen bonds : angle 5.13393 ( 3528) link_BETA1-4 : bond 0.00308 ( 24) link_BETA1-4 : angle 1.13939 ( 72) link_NAG-ASN : bond 0.00239 ( 51) link_NAG-ASN : angle 1.29617 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6798.34 seconds wall clock time: 117 minutes 33.11 seconds (7053.11 seconds total)