Starting phenix.real_space_refine on Fri Mar 6 15:39:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wtf_32784/03_2026/7wtf_32784.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wtf_32784/03_2026/7wtf_32784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wtf_32784/03_2026/7wtf_32784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wtf_32784/03_2026/7wtf_32784.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wtf_32784/03_2026/7wtf_32784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wtf_32784/03_2026/7wtf_32784.map" } resolution = 3.0 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= -0.002 sd= 0.100 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 20372 2.51 5 N 5254 2.21 5 O 6279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32049 Number of models: 1 Model: "" Number of chains: 32 Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "D" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "G" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "J" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "K" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} 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: "E" 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: "F" 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: 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" 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: "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: "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: "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: "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: 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: "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: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 7.37, per 1000 atoms: 0.23 Number of scatterers: 32049 At special positions: 0 Unit cell: (150.8, 145.6, 251.68, 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 6279 8.00 N 5254 7.00 C 20372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 293 " - pdb=" SG CYS B 303 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 434 " distance=2.03 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 490 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 651 " distance=2.02 Simple disulfide: pdb=" SG CYS B 664 " - pdb=" SG CYS B 673 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 762 " distance=2.03 Simple disulfide: pdb=" SG CYS B 745 " - pdb=" SG CYS B 751 " distance=2.03 Simple disulfide: pdb=" SG CYS B1034 " - pdb=" SG CYS B1045 " distance=2.03 Simple disulfide: pdb=" SG CYS B1084 " - pdb=" SG CYS B1128 " 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 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 338 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 381 " - pdb=" SG CYS C 434 " distance=2.03 Simple disulfide: pdb=" SG CYS C 393 " - pdb=" SG CYS C 527 " distance=2.03 Simple disulfide: pdb=" SG CYS C 482 " - pdb=" SG CYS C 490 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 651 " distance=2.02 Simple disulfide: pdb=" SG CYS C 664 " - pdb=" SG CYS C 673 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 762 " distance=2.03 Simple disulfide: pdb=" SG CYS C 745 " - pdb=" SG CYS C 751 " distance=2.03 Simple disulfide: pdb=" SG CYS C1034 " - pdb=" SG CYS C1045 " distance=2.03 Simple disulfide: pdb=" SG CYS C1084 " - pdb=" SG CYS C1128 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 163 " distance=2.03 Simple disulfide: pdb=" SG CYS D 293 " - pdb=" SG CYS D 303 " distance=2.03 Simple disulfide: pdb=" SG CYS D 338 " - pdb=" SG CYS D 363 " distance=2.04 Simple disulfide: pdb=" SG CYS D 381 " - pdb=" SG CYS D 434 " distance=2.04 Simple disulfide: pdb=" SG CYS D 393 " - pdb=" SG CYS D 527 " distance=2.03 Simple disulfide: pdb=" SG CYS D 482 " - pdb=" SG CYS D 490 " distance=2.03 Simple disulfide: pdb=" SG CYS D 619 " - pdb=" SG CYS D 651 " distance=2.03 Simple disulfide: pdb=" SG CYS D 664 " - pdb=" SG CYS D 673 " distance=2.03 Simple disulfide: pdb=" SG CYS D 740 " - pdb=" SG CYS D 762 " distance=2.04 Simple disulfide: pdb=" SG CYS D 745 " - pdb=" SG CYS D 751 " distance=2.03 Simple disulfide: pdb=" SG CYS D1034 " - pdb=" SG CYS D1045 " distance=2.03 Simple disulfide: pdb=" SG CYS D1084 " - pdb=" SG CYS D1128 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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 a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A 1 " - " ASN B 719 " " NAG B1201 " - " ASN B1160 " " NAG B1202 " - " ASN B 17 " " NAG B1203 " - " ASN B 61 " " NAG B1204 " - " ASN B 605 " " NAG B1205 " - " ASN B 659 " " NAG B1206 " - " ASN B 618 " " NAG B1207 " - " ASN B 711 " " NAG B1208 " - " ASN B 122 " " NAG B1209 " - " ASN B 149 " " NAG B1210 " - " ASN B 333 " " NAG B1211 " - " ASN B 284 " " NAG C1201 " - " ASN C1160 " " NAG C1202 " - " ASN C 125 " " NAG C1203 " - " ASN C 17 " " NAG C1204 " - " ASN C 61 " " NAG C1205 " - " ASN C 605 " " NAG C1206 " - " ASN C 659 " " NAG C1207 " - " ASN C 711 " " NAG C1208 " - " ASN C 146 " " NAG C1209 " - " ASN C 162 " " NAG C1210 " - " ASN C 618 " " NAG D1201 " - " ASN D1160 " " NAG D1202 " - " ASN D 17 " " NAG D1203 " - " ASN D 61 " " NAG D1204 " - " ASN D 605 " " NAG D1205 " - " ASN D 659 " " NAG D1206 " - " ASN D 711 " " NAG D1207 " - " ASN D 146 " " NAG D1208 " - " ASN D 284 " " NAG D1209 " - " ASN D 618 " " NAG E 1 " - " ASN B 803 " " NAG F 1 " - " ASN B1100 " " NAG M 1 " - " ASN B1136 " " NAG N 1 " - " ASN B1076 " " NAG P 1 " - " ASN C 719 " " NAG Q 1 " - " ASN C 803 " " NAG R 1 " - " ASN C1100 " " NAG S 1 " - " ASN C1136 " " NAG T 1 " - " ASN C 284 " " NAG U 1 " - " ASN C1076 " " NAG V 1 " - " ASN C 333 " " NAG W 1 " - " ASN D 233 " " NAG X 1 " - " ASN D 719 " " NAG Y 1 " - " ASN D1076 " " NAG Z 1 " - " ASN D 803 " " NAG a 1 " - " ASN D1100 " " NAG b 1 " - " ASN D1136 " " NAG c 1 " - " ASN D 333 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.2 seconds 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7398 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 61 sheets defined 20.0% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'B' and resid 296 through 306 Processing helix chain 'B' and resid 339 through 345 removed outlier: 4.041A pdb=" N VAL B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.575A pdb=" N LEU B 389 " --> pdb=" O PRO B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.666A pdb=" N ALA B 413 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 423 Processing helix chain 'B' and resid 545 through 548 Processing helix chain 'B' and resid 635 through 640 removed outlier: 4.090A pdb=" N THR B 640 " --> pdb=" O VAL B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 748 through 755 Processing helix chain 'B' and resid 756 through 759 removed outlier: 3.713A pdb=" N GLY B 759 " --> pdb=" O LEU B 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 756 through 759' Processing helix chain 'B' and resid 760 through 785 removed outlier: 3.843A pdb=" N ASP B 777 " --> pdb=" O ALA B 773 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 783 " --> pdb=" O ASN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 825 Processing helix chain 'B' and resid 851 through 855 removed outlier: 3.532A pdb=" N ALA B 854 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN B 855 " --> pdb=" O ILE B 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 851 through 855' Processing helix chain 'B' and resid 868 through 886 removed outlier: 3.886A pdb=" N GLN B 874 " --> pdb=" O GLU B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 892 Processing helix chain 'B' and resid 899 through 912 removed outlier: 3.751A pdb=" N ALA B 905 " --> pdb=" O PRO B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 920 removed outlier: 3.915A pdb=" N TYR B 919 " --> pdb=" O GLN B 915 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 920 " --> pdb=" O ASN B 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 915 through 920' Processing helix chain 'B' and resid 921 through 942 removed outlier: 3.628A pdb=" N LYS B 935 " --> pdb=" O SER B 931 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 936 " --> pdb=" O ALA B 932 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN B 937 " --> pdb=" O ILE B 933 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 938 " --> pdb=" O GLY B 934 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 941 " --> pdb=" O GLN B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 967 removed outlier: 3.794A pdb=" N ASP B 952 " --> pdb=" O GLY B 948 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL B 953 " --> pdb=" O LYS B 949 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 954 " --> pdb=" O LEU B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 970 No H-bonds generated for 'chain 'B' and resid 968 through 970' Processing helix chain 'B' and resid 979 through 984 Processing helix chain 'B' and resid 987 through 995 removed outlier: 3.540A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 993 " --> pdb=" O PRO B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1000 removed outlier: 3.512A pdb=" N THR B1000 " --> pdb=" O ASP B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1034 removed outlier: 3.515A pdb=" N THR B1008 " --> pdb=" O GLN B1004 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B1009 " --> pdb=" O SER B1005 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B1023 " --> pdb=" O GLU B1019 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1149 removed outlier: 4.180A pdb=" N GLU B1146 " --> pdb=" O PRO B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1150 through 1163 removed outlier: 3.592A pdb=" N ASP B1155 " --> pdb=" O LYS B1151 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B1156 " --> pdb=" O GLU B1152 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HIS B1161 " --> pdb=" O TYR B1157 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B1162 " --> pdb=" O PHE B1158 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER B1163 " --> pdb=" O LYS B1159 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 340 through 345 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.029A pdb=" N ASN C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 removed outlier: 3.524A pdb=" N ILE C 412 " --> pdb=" O GLU C 408 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 413 " --> pdb=" O VAL C 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 408 through 413' Processing helix chain 'C' and resid 419 through 424 removed outlier: 3.598A pdb=" N TYR C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN C 424 " --> pdb=" O ILE C 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 419 through 424' Processing helix chain 'C' and resid 440 through 445 removed outlier: 3.788A pdb=" N SER C 445 " --> pdb=" O ASN C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 746 removed outlier: 3.952A pdb=" N ILE C 744 " --> pdb=" O CYS C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 756 removed outlier: 3.697A pdb=" N SER C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN C 753 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU C 754 " --> pdb=" O GLU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 759 No H-bonds generated for 'chain 'C' and resid 757 through 759' Processing helix chain 'C' and resid 762 through 784 removed outlier: 3.553A pdb=" N ASP C 777 " --> pdb=" O ALA C 773 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C 780 " --> pdb=" O GLN C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 825 removed outlier: 3.569A pdb=" N LEU C 823 " --> pdb=" O PRO C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 886 removed outlier: 3.544A pdb=" N ALA C 873 " --> pdb=" O ASP C 869 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN C 874 " --> pdb=" O GLU C 870 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 884 " --> pdb=" O LEU C 880 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR C 885 " --> pdb=" O ALA C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 912 removed outlier: 3.956A pdb=" N ALA C 905 " --> pdb=" O PRO C 901 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE C 911 " --> pdb=" O ARG C 907 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 912 " --> pdb=" O PHE C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 920 removed outlier: 3.697A pdb=" N TYR C 919 " --> pdb=" O GLN C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 940 removed outlier: 3.569A pdb=" N LYS C 935 " --> pdb=" O SER C 931 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE C 936 " --> pdb=" O ALA C 932 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN C 937 " --> pdb=" O ILE C 933 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C 938 " --> pdb=" O GLY C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 946 removed outlier: 3.911A pdb=" N ALA C 946 " --> pdb=" O THR C 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 943 through 946' Processing helix chain 'C' and resid 947 through 966 removed outlier: 4.151A pdb=" N VAL C 953 " --> pdb=" O LYS C 949 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 954 " --> pdb=" O LEU C 950 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN C 957 " --> pdb=" O VAL C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 985 removed outlier: 3.615A pdb=" N PHE C 983 " --> pdb=" O LEU C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 995 removed outlier: 3.646A pdb=" N GLU C 992 " --> pdb=" O PRO C 988 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 993 " --> pdb=" O PRO C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1034 removed outlier: 3.806A pdb=" N ARG C1002 " --> pdb=" O LEU C 998 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C1003 " --> pdb=" O ILE C 999 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C1026 " --> pdb=" O ALA C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1149 removed outlier: 3.917A pdb=" N GLU C1146 " --> pdb=" O PRO C1142 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C1149 " --> pdb=" O PRO C1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 1150 through 1159 removed outlier: 3.701A pdb=" N ASP C1155 " --> pdb=" O LYS C1151 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C1156 " --> pdb=" O GLU C1152 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 340 through 345 removed outlier: 3.930A pdb=" N PHE D 344 " --> pdb=" O PHE D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'D' and resid 407 through 413 removed outlier: 4.120A pdb=" N GLN D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 626 removed outlier: 3.947A pdb=" N ILE D 626 " --> pdb=" O PRO D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 746 removed outlier: 3.520A pdb=" N TYR D 743 " --> pdb=" O ASP D 739 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS D 745 " --> pdb=" O THR D 741 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY D 746 " --> pdb=" O MET D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 756 removed outlier: 4.096A pdb=" N ASN D 753 " --> pdb=" O THR D 749 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 754 " --> pdb=" O GLU D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 759 No H-bonds generated for 'chain 'D' and resid 757 through 759' Processing helix chain 'D' and resid 760 through 785 removed outlier: 3.650A pdb=" N GLN D 764 " --> pdb=" O SER D 760 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 765 " --> pdb=" O PHE D 761 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 766 " --> pdb=" O CYS D 762 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN D 776 " --> pdb=" O ILE D 772 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP D 777 " --> pdb=" O ALA D 773 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR D 780 " --> pdb=" O GLN D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 828 removed outlier: 3.523A pdb=" N ASN D 826 " --> pdb=" O ASP D 822 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 886 removed outlier: 3.814A pdb=" N THR D 885 " --> pdb=" O ALA D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 892 removed outlier: 3.535A pdb=" N GLY D 891 " --> pdb=" O TRP D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 912 removed outlier: 3.709A pdb=" N ALA D 905 " --> pdb=" O PRO D 901 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR D 906 " --> pdb=" O MET D 902 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 911 " --> pdb=" O ARG D 907 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 912 " --> pdb=" O PHE D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 920 removed outlier: 3.696A pdb=" N TYR D 919 " --> pdb=" O GLN D 915 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 943 removed outlier: 3.550A pdb=" N ILE D 936 " --> pdb=" O ALA D 932 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN D 937 " --> pdb=" O ILE D 933 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP D 938 " --> pdb=" O GLY D 934 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR D 943 " --> pdb=" O SER D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 946 No H-bonds generated for 'chain 'D' and resid 944 through 946' Processing helix chain 'D' and resid 947 through 967 removed outlier: 3.828A pdb=" N VAL D 953 " --> pdb=" O LYS D 949 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR D 963 " --> pdb=" O GLN D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 968 through 970 No H-bonds generated for 'chain 'D' and resid 968 through 970' Processing helix chain 'D' and resid 980 through 985 removed outlier: 3.750A pdb=" N SER D 984 " --> pdb=" O ASN D 980 " (cutoff:3.500A) Processing helix chain 'D' and resid 990 through 1000 removed outlier: 3.657A pdb=" N LEU D 998 " --> pdb=" O GLN D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1034 removed outlier: 3.536A pdb=" N LEU D1026 " --> pdb=" O ALA D1022 " (cutoff:3.500A) Processing helix chain 'D' and resid 1142 through 1162 removed outlier: 4.259A pdb=" N GLU D1146 " --> pdb=" O PRO D1142 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.426A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 46 through 49 removed outlier: 5.903A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.657A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 44 through 46 Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.023A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ASN B 61 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR B 271 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.248A pdb=" N ASP B 289 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 168 through 172 removed outlier: 4.089A pdb=" N ILE B 105 " --> pdb=" O GLN B 241 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 241 " --> pdb=" O ILE B 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 313 through 320 removed outlier: 5.769A pdb=" N ILE B 314 " --> pdb=" O THR B 601 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR B 601 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLN B 316 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B 599 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 318 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AB1, first strand: chain 'B' and resid 358 through 360 Processing sheet with id=AB2, first strand: chain 'B' and resid 358 through 360 Processing sheet with id=AB3, first strand: chain 'B' and resid 454 through 456 Processing sheet with id=AB4, first strand: chain 'B' and resid 475 through 476 Processing sheet with id=AB5, first strand: chain 'B' and resid 567 through 569 Processing sheet with id=AB6, first strand: chain 'B' and resid 656 through 657 removed outlier: 5.972A pdb=" N GLU B 656 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 698 " --> pdb=" O GLU B 656 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 697 " --> pdb=" O CYS B 673 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 672 " --> pdb=" O ILE B 668 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 703 through 706 Processing sheet with id=AB8, first strand: chain 'B' and resid 713 through 721 removed outlier: 6.521A pdb=" N SER B 713 " --> pdb=" O THR B1078 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR B1078 " --> pdb=" O SER B 713 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA B 715 " --> pdb=" O ASN B1076 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASN B1076 " --> pdb=" O ALA B 715 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU B1074 " --> pdb=" O PRO B 717 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN B 719 " --> pdb=" O ALA B1072 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B1078 " --> pdb=" O SER B1099 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B1080 " --> pdb=" O PHE B1097 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE B1097 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 724 through 730 Processing sheet with id=AC1, first strand: chain 'B' and resid 736 through 738 removed outlier: 3.550A pdb=" N THR B 861 " --> pdb=" O SER B 737 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 790 through 792 removed outlier: 5.406A pdb=" N ILE B 790 " --> pdb=" O ASN C 705 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 1122 through 1124 Processing sheet with id=AC4, first strand: chain 'C' and resid 27 through 31 removed outlier: 7.830A pdb=" N ASN C 61 " --> pdb=" O TYR C 271 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TYR C 271 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 96 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN C 185 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE C 198 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP C 227 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE C 200 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 225 " --> pdb=" O ILE C 200 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.573A pdb=" N ALA D 577 " --> pdb=" O GLY D 568 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR D 590 " --> pdb=" O VAL D 553 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.805A pdb=" N ASP C 289 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AC8, first strand: chain 'C' and resid 165 through 169 removed outlier: 5.701A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY C 103 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 313 through 321 removed outlier: 5.283A pdb=" N ILE C 314 " --> pdb=" O THR C 601 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR C 601 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLN C 316 " --> pdb=" O VAL C 599 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL C 599 " --> pdb=" O GLN C 316 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER C 318 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 597 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 652 " --> pdb=" O PHE C 645 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C 645 " --> pdb=" O LEU C 652 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 326 through 330 removed outlier: 7.454A pdb=" N GLU C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ASN C 544 " --> pdb=" O GLU C 326 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE C 328 " --> pdb=" O ASN C 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 358 through 360 removed outlier: 3.952A pdb=" N ILE C 360 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 397 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 511 " --> pdb=" O TRP C 438 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP C 438 " --> pdb=" O ARG C 511 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 475 through 476 removed outlier: 3.630A pdb=" N TYR C 475 " --> pdb=" O TYR C 491 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 553 through 556 removed outlier: 3.656A pdb=" N THR C 590 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA C 577 " --> pdb=" O GLY C 568 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 656 through 657 removed outlier: 6.118A pdb=" N GLU C 656 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N THR C 698 " --> pdb=" O GLU C 656 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE C 672 " --> pdb=" O ILE C 668 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 713 through 730 removed outlier: 6.548A pdb=" N SER C 713 " --> pdb=" O THR C1078 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR C1078 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 715 " --> pdb=" O ASN C1076 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN C1076 " --> pdb=" O ALA C 715 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU C1074 " --> pdb=" O PRO C 717 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLY C1061 " --> pdb=" O SER C1057 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N SER C1057 " --> pdb=" O GLY C1061 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL C1063 " --> pdb=" O PRO C1055 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU C1065 " --> pdb=" O SER C1053 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER C1053 " --> pdb=" O LEU C1065 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL C1067 " --> pdb=" O LEU C1051 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 713 through 730 removed outlier: 6.548A pdb=" N SER C 713 " --> pdb=" O THR C1078 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR C1078 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 715 " --> pdb=" O ASN C1076 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN C1076 " --> pdb=" O ALA C 715 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU C1074 " --> pdb=" O PRO C 717 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C1080 " --> pdb=" O PHE C1097 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE C1097 " --> pdb=" O ALA C1080 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 737 through 738 Processing sheet with id=AD9, first strand: chain 'C' and resid 789 through 792 removed outlier: 6.033A pdb=" N ILE C 790 " --> pdb=" O ASN D 705 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 1122 through 1124 Processing sheet with id=AE2, first strand: chain 'D' and resid 27 through 31 removed outlier: 7.993A pdb=" N ASN D 61 " --> pdb=" O TYR D 271 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR D 271 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA D 266 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N SER D 202 " --> pdb=" O PRO D 224 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N HIS D 204 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N LEU D 222 " --> pdb=" O HIS D 204 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL D 36 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.722A pdb=" N ASP D 289 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AE5, first strand: chain 'D' and resid 168 through 169 Processing sheet with id=AE6, first strand: chain 'D' and resid 313 through 321 removed outlier: 5.214A pdb=" N ILE D 314 " --> pdb=" O THR D 601 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR D 601 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN D 316 " --> pdb=" O VAL D 599 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL D 599 " --> pdb=" O GLN D 316 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N SER D 318 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL D 597 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS D 651 " --> pdb=" O TYR D 614 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY D 650 " --> pdb=" O THR D 647 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 358 through 360 removed outlier: 3.982A pdb=" N ALA D 399 " --> pdb=" O LYS D 358 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 360 " --> pdb=" O VAL D 397 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 363 through 364 removed outlier: 6.832A pdb=" N CYS D 363 " --> pdb=" O CYS D 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 402 through 404 removed outlier: 3.878A pdb=" N ILE D 404 " --> pdb=" O TYR D 510 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG D 511 " --> pdb=" O TRP D 438 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP D 438 " --> pdb=" O ARG D 511 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 513 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE D 436 " --> pdb=" O VAL D 513 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 454 through 456 Processing sheet with id=AF2, first strand: chain 'D' and resid 475 through 476 Processing sheet with id=AF3, first strand: chain 'D' and resid 544 through 545 Processing sheet with id=AF4, first strand: chain 'D' and resid 656 through 657 removed outlier: 6.142A pdb=" N GLU D 656 " --> pdb=" O ALA D 696 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR D 698 " --> pdb=" O GLU D 656 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR D 697 " --> pdb=" O CYS D 673 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE D 672 " --> pdb=" O ILE D 668 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 713 through 721 removed outlier: 6.536A pdb=" N SER D 713 " --> pdb=" O THR D1078 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR D1078 " --> pdb=" O SER D 713 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA D 715 " --> pdb=" O ASN D1076 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN D1076 " --> pdb=" O ALA D 715 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU D1074 " --> pdb=" O PRO D 717 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR D1069 " --> pdb=" O HIS D1050 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N HIS D1050 " --> pdb=" O TYR D1069 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 724 through 730 removed outlier: 3.627A pdb=" N ALA D1080 " --> pdb=" O PHE D1097 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE D1097 " --> pdb=" O ALA D1080 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 737 through 738 Processing sheet with id=AF8, first strand: chain 'D' and resid 1122 through 1127 removed outlier: 3.603A pdb=" N SER D1125 " --> pdb=" O ALA D1089 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA D1089 " --> pdb=" O SER D1125 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 3 through 6 removed outlier: 4.898A pdb=" N SER G 77 " --> pdb=" O ALA G 24 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.096A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 19 through 24 removed outlier: 3.786A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE J 75 " --> pdb=" O VAL J 19 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 45 through 46 Processing sheet with id=AG4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AG5, first strand: chain 'I' and resid 47 through 51 removed outlier: 7.171A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 21 through 24 Processing sheet with id=AG7, first strand: chain 'K' and resid 44 through 48 removed outlier: 6.572A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 950 hydrogen bonds defined for protein. 2535 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: 7.81 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 5146 1.28 - 1.41: 8250 1.41 - 1.55: 19155 1.55 - 1.69: 56 1.69 - 1.82: 186 Bond restraints: 32793 Sorted by residual: bond pdb=" C PRO C 899 " pdb=" O PRO C 899 " ideal model delta sigma weight residual 1.233 1.140 0.093 1.13e-02 7.83e+03 6.82e+01 bond pdb=" C PRO B 899 " pdb=" O PRO B 899 " ideal model delta sigma weight residual 1.233 1.144 0.089 1.13e-02 7.83e+03 6.19e+01 bond pdb=" C PRO D 899 " pdb=" O PRO D 899 " ideal model delta sigma weight residual 1.233 1.150 0.084 1.10e-02 8.26e+03 5.79e+01 bond pdb=" C PRO C 901 " pdb=" O PRO C 901 " ideal model delta sigma weight residual 1.237 1.142 0.096 1.32e-02 5.74e+03 5.25e+01 bond pdb=" C PRO D 901 " pdb=" O PRO D 901 " ideal model delta sigma weight residual 1.238 1.154 0.083 1.24e-02 6.50e+03 4.51e+01 ... (remaining 32788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 43032 2.58 - 5.16: 1324 5.16 - 7.73: 185 7.73 - 10.31: 40 10.31 - 12.89: 9 Bond angle restraints: 44590 Sorted by residual: angle pdb=" N PRO D 988 " pdb=" CA PRO D 988 " pdb=" C PRO D 988 " ideal model delta sigma weight residual 110.70 123.15 -12.45 1.22e+00 6.72e-01 1.04e+02 angle pdb=" C ASN C 544 " pdb=" CA ASN C 544 " pdb=" CB ASN C 544 " ideal model delta sigma weight residual 111.82 101.11 10.71 1.38e+00 5.25e-01 6.02e+01 angle pdb=" N SER B 942 " pdb=" CA SER B 942 " pdb=" C SER B 942 " ideal model delta sigma weight residual 113.20 103.92 9.28 1.21e+00 6.83e-01 5.88e+01 angle pdb=" N ALA B 946 " pdb=" CA ALA B 946 " pdb=" C ALA B 946 " ideal model delta sigma weight residual 111.82 103.44 8.38 1.16e+00 7.43e-01 5.21e+01 angle pdb=" C THR B 943 " pdb=" CA THR B 943 " pdb=" CB THR B 943 " ideal model delta sigma weight residual 110.71 121.56 -10.85 1.53e+00 4.27e-01 5.03e+01 ... (remaining 44585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.62: 19104 23.62 - 47.24: 1186 47.24 - 70.86: 142 70.86 - 94.49: 65 94.49 - 118.11: 34 Dihedral angle restraints: 20531 sinusoidal: 9008 harmonic: 11523 Sorted by residual: dihedral pdb=" CA ASN D 145 " pdb=" C ASN D 145 " pdb=" N ASN D 146 " pdb=" CA ASN D 146 " ideal model delta harmonic sigma weight residual -180.00 -70.15 -109.85 0 5.00e+00 4.00e-02 4.83e+02 dihedral pdb=" CA ASP C 142 " pdb=" C ASP C 142 " pdb=" N HIS C 143 " pdb=" CA HIS C 143 " ideal model delta harmonic sigma weight residual 180.00 70.18 109.82 0 5.00e+00 4.00e-02 4.82e+02 dihedral pdb=" CB CYS D 740 " pdb=" SG CYS D 740 " pdb=" SG CYS D 762 " pdb=" CB CYS D 762 " ideal model delta sinusoidal sigma weight residual 93.00 3.84 89.16 1 1.00e+01 1.00e-02 9.46e+01 ... (remaining 20528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 5051 0.155 - 0.309: 141 0.309 - 0.464: 6 0.464 - 0.618: 2 0.618 - 0.773: 1 Chirality restraints: 5201 Sorted by residual: chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN D 333 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" C1 NAG C1208 " pdb=" ND2 ASN C 146 " pdb=" C2 NAG C1208 " pdb=" O5 NAG C1208 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CA PRO D 988 " pdb=" N PRO D 988 " pdb=" C PRO D 988 " pdb=" CB PRO D 988 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 5198 not shown) Planarity restraints: 5717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 147 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C LYS D 147 " -0.063 2.00e-02 2.50e+03 pdb=" O LYS D 147 " 0.023 2.00e-02 2.50e+03 pdb=" N SER D 148 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 941 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C SER B 941 " -0.060 2.00e-02 2.50e+03 pdb=" O SER B 941 " 0.022 2.00e-02 2.50e+03 pdb=" N SER B 942 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 762 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C CYS D 762 " -0.056 2.00e-02 2.50e+03 pdb=" O CYS D 762 " 0.020 2.00e-02 2.50e+03 pdb=" N THR D 763 " 0.019 2.00e-02 2.50e+03 ... (remaining 5714 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 8677 2.80 - 3.33: 26820 3.33 - 3.85: 52153 3.85 - 4.38: 58528 4.38 - 4.90: 101123 Nonbonded interactions: 247301 Sorted by model distance: nonbonded pdb=" O GLY C 882 " pdb=" OG SER C 886 " model vdw 2.278 3.040 nonbonded pdb=" O VAL D 610 " pdb=" OH TYR D 638 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR B 647 " pdb=" O GLY B 650 " model vdw 2.286 3.040 nonbonded pdb=" O ASP H 112 " pdb=" OH TYR L 49 " model vdw 2.290 3.040 nonbonded pdb=" OG SER H 21 " pdb=" OG1 THR H 78 " model vdw 2.298 3.040 ... (remaining 247296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'B' and resid 14 through 1209) selection = (chain 'C' and resid 14 through 1209) selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'M' selection = chain 'R' selection = chain 'S' selection = chain 'a' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.410 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 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 : 0.006 0.103 32913 Z= 0.391 Angle : 1.026 15.177 44902 Z= 0.579 Chirality : 0.065 0.773 5201 Planarity : 0.007 0.082 5668 Dihedral : 15.823 118.107 12998 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.06 % Favored : 92.74 % Rotamer: Outliers : 0.52 % Allowed : 1.16 % Favored : 98.32 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.03 (0.12), residues: 3924 helix: -3.29 (0.12), residues: 669 sheet: -0.40 (0.19), residues: 783 loop : -2.30 (0.11), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 187 TYR 0.045 0.002 TYR B 455 PHE 0.030 0.002 PHE C 106 TRP 0.037 0.002 TRP C 260 HIS 0.013 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00639 (32793) covalent geometry : angle 1.00946 (44590) SS BOND : bond 0.00360 ( 45) SS BOND : angle 1.52739 ( 90) hydrogen bonds : bond 0.23343 ( 932) hydrogen bonds : angle 9.01661 ( 2535) Misc. bond : bond 0.00059 ( 1) link_BETA1-4 : bond 0.00851 ( 25) link_BETA1-4 : angle 2.19906 ( 75) link_NAG-ASN : bond 0.00713 ( 49) link_NAG-ASN : angle 2.94654 ( 147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 436 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 MET cc_start: 0.1742 (tpt) cc_final: 0.1148 (mtm) REVERT: B 360 ILE cc_start: 0.7982 (mt) cc_final: 0.7722 (mm) REVERT: B 367 TYR cc_start: 0.7255 (m-80) cc_final: 0.6924 (m-80) REVERT: B 983 PHE cc_start: 0.6700 (m-10) cc_final: 0.6393 (m-10) REVERT: C 117 LEU cc_start: 0.6081 (mt) cc_final: 0.5562 (tt) REVERT: C 142 ASP cc_start: 0.1998 (OUTLIER) cc_final: 0.1052 (t0) REVERT: C 823 LEU cc_start: 0.8218 (mt) cc_final: 0.7937 (mp) REVERT: D 1074 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7225 (pt0) outliers start: 18 outliers final: 8 residues processed: 449 average time/residue: 0.5972 time to fit residues: 323.6621 Evaluate side-chains 221 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 211 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 1074 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.0030 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 91 GLN B 49 HIS B 362 ASN B 615 GLN B 677 GLN B 753 ASN B 757 GLN B 764 GLN B 903 GLN B 909 ASN B1121 ASN C 99 ASN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN C 546 ASN C 582 GLN C 903 GLN C 927 ASN C 967 GLN C1012 GLN C1115 GLN D 14 GLN D 273 GLN D 424 ASN D 582 GLN D 615 GLN D 786 GLN D1004 GLN D1121 ASN I 31 ASN K 31 ASN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.215799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.162765 restraints weight = 48894.560| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.73 r_work: 0.3565 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32913 Z= 0.130 Angle : 0.672 14.321 44902 Z= 0.327 Chirality : 0.048 0.623 5201 Planarity : 0.005 0.057 5668 Dihedral : 10.029 105.327 5851 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.58 % Favored : 94.34 % Rotamer: Outliers : 1.85 % Allowed : 9.96 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.18 (0.12), residues: 3924 helix: -1.13 (0.18), residues: 683 sheet: -0.08 (0.19), residues: 790 loop : -2.13 (0.11), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 44 TYR 0.018 0.001 TYR B 170 PHE 0.020 0.001 PHE B 594 TRP 0.025 0.001 TRP C 260 HIS 0.013 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00290 (32793) covalent geometry : angle 0.64554 (44590) SS BOND : bond 0.00356 ( 45) SS BOND : angle 1.52019 ( 90) hydrogen bonds : bond 0.04896 ( 932) hydrogen bonds : angle 6.25612 ( 2535) Misc. bond : bond 0.00026 ( 1) link_BETA1-4 : bond 0.00623 ( 25) link_BETA1-4 : angle 2.03525 ( 75) link_NAG-ASN : bond 0.00780 ( 49) link_NAG-ASN : angle 2.82294 ( 147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 205 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 360 ILE cc_start: 0.8076 (mt) cc_final: 0.7854 (mm) REVERT: B 367 TYR cc_start: 0.7739 (m-80) cc_final: 0.7461 (m-80) REVERT: B 857 PHE cc_start: 0.6956 (m-80) cc_final: 0.6751 (m-80) REVERT: C 167 TYR cc_start: 0.7558 (t80) cc_final: 0.7282 (t80) REVERT: C 174 MET cc_start: 0.3023 (mtt) cc_final: 0.1240 (mmt) REVERT: C 316 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8326 (tm-30) REVERT: C 570 ASP cc_start: 0.7912 (p0) cc_final: 0.7518 (p0) REVERT: C 677 GLN cc_start: 0.7693 (mm110) cc_final: 0.7316 (mm-40) REVERT: D 1121 ASN cc_start: 0.6991 (m-40) cc_final: 0.6606 (m110) REVERT: G 81 MET cc_start: 0.1905 (tpt) cc_final: 0.0865 (ptm) REVERT: K 4 MET cc_start: 0.0882 (ptp) cc_final: -0.0524 (ptt) outliers start: 64 outliers final: 24 residues processed: 250 average time/residue: 0.4773 time to fit residues: 150.1024 Evaluate side-chains 192 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 363 CYS Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain J residue 77 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 40 optimal weight: 5.9990 chunk 305 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 88 optimal weight: 0.0470 chunk 351 optimal weight: 40.0000 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 chunk 188 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN B 49 HIS B 362 ASN C 789 GLN D 14 GLN D 99 ASN D 273 GLN D 962 ASN J 55 GLN I 31 ASN ** K 55 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 = 0.4619 r_free = 0.4619 target = 0.213231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.156052 restraints weight = 48319.674| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.62 r_work: 0.3511 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32913 Z= 0.155 Angle : 0.652 12.124 44902 Z= 0.317 Chirality : 0.048 0.479 5201 Planarity : 0.004 0.056 5668 Dihedral : 8.244 103.618 5839 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.86 % Favored : 94.09 % Rotamer: Outliers : 2.43 % Allowed : 12.60 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.83 (0.13), residues: 3924 helix: -0.26 (0.20), residues: 691 sheet: -0.07 (0.18), residues: 811 loop : -2.02 (0.11), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 44 TYR 0.018 0.001 TYR D 267 PHE 0.019 0.001 PHE C 219 TRP 0.017 0.002 TRP B 438 HIS 0.005 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00366 (32793) covalent geometry : angle 0.62574 (44590) SS BOND : bond 0.00348 ( 45) SS BOND : angle 1.58899 ( 90) hydrogen bonds : bond 0.04344 ( 932) hydrogen bonds : angle 5.85146 ( 2535) Misc. bond : bond 0.00041 ( 1) link_BETA1-4 : bond 0.00586 ( 25) link_BETA1-4 : angle 2.03983 ( 75) link_NAG-ASN : bond 0.00702 ( 49) link_NAG-ASN : angle 2.73543 ( 147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 184 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 MET cc_start: 0.0372 (mtm) cc_final: -0.1191 (mtt) REVERT: L 22 THR cc_start: 0.5613 (t) cc_final: 0.4987 (m) REVERT: B 54 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6808 (mt) REVERT: B 360 ILE cc_start: 0.8189 (mt) cc_final: 0.7890 (mm) REVERT: B 367 TYR cc_start: 0.7762 (m-80) cc_final: 0.7503 (m-80) REVERT: C 174 MET cc_start: 0.3208 (mtt) cc_final: 0.1733 (mmp) REVERT: C 197 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.7129 (t80) REVERT: C 317 THR cc_start: 0.8661 (m) cc_final: 0.8418 (p) REVERT: C 570 ASP cc_start: 0.8045 (p0) cc_final: 0.7667 (p0) REVERT: C 677 GLN cc_start: 0.7734 (mm110) cc_final: 0.7384 (mm-40) REVERT: C 1121 ASN cc_start: 0.8193 (m-40) cc_final: 0.7977 (m110) REVERT: D 549 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7170 (mmmt) REVERT: D 567 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6407 (m-80) REVERT: I 48 MET cc_start: 0.1942 (mpt) cc_final: 0.1431 (mmm) REVERT: I 81 MET cc_start: -0.0904 (OUTLIER) cc_final: -0.2310 (ptm) REVERT: K 4 MET cc_start: 0.0649 (ptp) cc_final: -0.0629 (ptt) outliers start: 84 outliers final: 44 residues processed: 247 average time/residue: 0.5443 time to fit residues: 165.8958 Evaluate side-chains 205 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 363 CYS Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 994 GLN Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain I residue 81 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 148 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 88 optimal weight: 0.0670 chunk 78 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 327 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS B 489 ASN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN D 14 GLN D1121 ASN J 37 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.209270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.152276 restraints weight = 47616.476| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.57 r_work: 0.3418 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 32913 Z= 0.248 Angle : 0.722 11.662 44902 Z= 0.354 Chirality : 0.050 0.455 5201 Planarity : 0.004 0.053 5668 Dihedral : 7.349 102.421 5838 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.29 % Favored : 93.65 % Rotamer: Outliers : 2.98 % Allowed : 14.91 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.86 (0.13), residues: 3924 helix: -0.17 (0.20), residues: 703 sheet: -0.16 (0.18), residues: 814 loop : -2.07 (0.12), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 44 TYR 0.029 0.002 TYR C 906 PHE 0.033 0.002 PHE C 106 TRP 0.020 0.002 TRP H 36 HIS 0.007 0.002 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00601 (32793) covalent geometry : angle 0.69632 (44590) SS BOND : bond 0.00455 ( 45) SS BOND : angle 1.91294 ( 90) hydrogen bonds : bond 0.04708 ( 932) hydrogen bonds : angle 5.95239 ( 2535) Misc. bond : bond 0.00028 ( 1) link_BETA1-4 : bond 0.00545 ( 25) link_BETA1-4 : angle 2.12900 ( 75) link_NAG-ASN : bond 0.00501 ( 49) link_NAG-ASN : angle 2.72770 ( 147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 183 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 360 ILE cc_start: 0.8350 (mt) cc_final: 0.8054 (mm) REVERT: B 367 TYR cc_start: 0.7769 (m-80) cc_final: 0.7521 (m-80) REVERT: C 174 MET cc_start: 0.3368 (mtt) cc_final: 0.2951 (mmp) REVERT: C 197 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7361 (t80) REVERT: C 570 ASP cc_start: 0.8055 (p0) cc_final: 0.7711 (p0) REVERT: C 677 GLN cc_start: 0.7809 (mm110) cc_final: 0.7439 (mm-40) REVERT: C 978 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8334 (m) REVERT: C 1052 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8739 (ptm) REVERT: D 549 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7422 (mmmt) REVERT: I 48 MET cc_start: 0.1913 (OUTLIER) cc_final: 0.1229 (mmm) outliers start: 103 outliers final: 54 residues processed: 266 average time/residue: 0.5009 time to fit residues: 167.0499 Evaluate side-chains 206 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 147 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 967 GLN Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1138 THR Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 363 CYS Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 81 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 258 optimal weight: 0.7980 chunk 349 optimal weight: 50.0000 chunk 173 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 276 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 386 optimal weight: 30.0000 chunk 214 optimal weight: 0.8980 chunk 259 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS B 362 ASN B1073 GLN B1121 ASN C 145 ASN C 238 GLN D 903 GLN D 994 GLN D1121 ASN G 31 ASN J 37 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.210719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.152905 restraints weight = 47926.228| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.61 r_work: 0.3436 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32913 Z= 0.140 Angle : 0.633 13.208 44902 Z= 0.308 Chirality : 0.047 0.411 5201 Planarity : 0.004 0.073 5668 Dihedral : 6.806 105.661 5838 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.50 % Rotamer: Outliers : 2.72 % Allowed : 16.36 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.65 (0.13), residues: 3924 helix: 0.23 (0.20), residues: 701 sheet: -0.10 (0.18), residues: 808 loop : -1.96 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 44 TYR 0.018 0.001 TYR D 267 PHE 0.024 0.001 PHE C 106 TRP 0.017 0.001 TRP C 149 HIS 0.008 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00330 (32793) covalent geometry : angle 0.60964 (44590) SS BOND : bond 0.00314 ( 45) SS BOND : angle 1.55824 ( 90) hydrogen bonds : bond 0.03883 ( 932) hydrogen bonds : angle 5.72390 ( 2535) Misc. bond : bond 0.00009 ( 1) link_BETA1-4 : bond 0.00512 ( 25) link_BETA1-4 : angle 1.88781 ( 75) link_NAG-ASN : bond 0.00484 ( 49) link_NAG-ASN : angle 2.49847 ( 147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 165 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.7630 (mmt90) cc_final: 0.7341 (mmt90) REVERT: B 360 ILE cc_start: 0.8303 (mt) cc_final: 0.8036 (mm) REVERT: B 367 TYR cc_start: 0.7730 (m-80) cc_final: 0.7479 (m-80) REVERT: B 756 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9037 (mp) REVERT: B 857 PHE cc_start: 0.7092 (m-80) cc_final: 0.6819 (m-80) REVERT: C 197 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7362 (t80) REVERT: C 570 ASP cc_start: 0.8093 (p0) cc_final: 0.7702 (p0) REVERT: C 677 GLN cc_start: 0.7813 (mm110) cc_final: 0.7430 (mm-40) REVERT: C 978 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8321 (m) REVERT: C 1052 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8509 (ptm) REVERT: C 1121 ASN cc_start: 0.8203 (m-40) cc_final: 0.8003 (m110) REVERT: D 54 LEU cc_start: 0.8915 (mt) cc_final: 0.8538 (mp) REVERT: D 549 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7363 (mmmt) REVERT: D 1121 ASN cc_start: 0.7978 (m-40) cc_final: 0.7659 (m110) REVERT: I 48 MET cc_start: 0.1964 (OUTLIER) cc_final: 0.1232 (mmm) outliers start: 94 outliers final: 48 residues processed: 237 average time/residue: 0.4656 time to fit residues: 141.0925 Evaluate side-chains 200 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 146 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 983 PHE Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain C residue 1138 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 81 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 370 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 344 optimal weight: 1.9990 chunk 1 optimal weight: 0.0060 chunk 9 optimal weight: 20.0000 chunk 239 optimal weight: 9.9990 chunk 250 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 317 optimal weight: 0.6980 chunk 244 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 91 GLN B 49 HIS B 362 ASN ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1073 GLN ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1121 ASN B1137 ASN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 994 GLN J 37 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.210951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.149616 restraints weight = 47684.095| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.62 r_work: 0.3455 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 32913 Z= 0.133 Angle : 0.620 11.794 44902 Z= 0.302 Chirality : 0.046 0.409 5201 Planarity : 0.004 0.054 5668 Dihedral : 6.496 107.934 5837 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.38 % Favored : 94.55 % Rotamer: Outliers : 2.78 % Allowed : 17.17 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.56 (0.13), residues: 3924 helix: 0.42 (0.21), residues: 703 sheet: -0.14 (0.18), residues: 831 loop : -1.93 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 44 TYR 0.019 0.001 TYR C 167 PHE 0.021 0.001 PHE C 106 TRP 0.025 0.001 TRP D 149 HIS 0.005 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00316 (32793) covalent geometry : angle 0.59874 (44590) SS BOND : bond 0.00413 ( 45) SS BOND : angle 1.61008 ( 90) hydrogen bonds : bond 0.03683 ( 932) hydrogen bonds : angle 5.63776 ( 2535) Misc. bond : bond 0.00006 ( 1) link_BETA1-4 : bond 0.00474 ( 25) link_BETA1-4 : angle 1.76662 ( 75) link_NAG-ASN : bond 0.00463 ( 49) link_NAG-ASN : angle 2.36707 ( 147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 156 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 22 THR cc_start: 0.5774 (OUTLIER) cc_final: 0.5198 (m) REVERT: B 44 ARG cc_start: 0.7602 (mmt90) cc_final: 0.7358 (mmt90) REVERT: B 360 ILE cc_start: 0.8320 (mt) cc_final: 0.8051 (mm) REVERT: B 756 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9008 (mp) REVERT: B 857 PHE cc_start: 0.7098 (m-80) cc_final: 0.6824 (m-80) REVERT: B 1103 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.7085 (p90) REVERT: C 117 LEU cc_start: 0.7365 (mt) cc_final: 0.6751 (tp) REVERT: C 197 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7247 (t80) REVERT: C 570 ASP cc_start: 0.8031 (p0) cc_final: 0.7704 (p0) REVERT: C 677 GLN cc_start: 0.7807 (mm110) cc_final: 0.7461 (mm-40) REVERT: C 978 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8299 (m) REVERT: C 1052 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8505 (ptm) REVERT: D 549 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7272 (mmmt) REVERT: G 81 MET cc_start: -0.0390 (tpp) cc_final: -0.0853 (ttt) REVERT: I 48 MET cc_start: 0.1818 (OUTLIER) cc_final: 0.1227 (mmm) outliers start: 96 outliers final: 50 residues processed: 236 average time/residue: 0.4709 time to fit residues: 142.2245 Evaluate side-chains 199 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 141 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1103 HIS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1138 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 739 ASP Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain I residue 48 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 255 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 386 optimal weight: 20.0000 chunk 209 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 327 optimal weight: 0.4980 chunk 295 optimal weight: 0.0070 chunk 87 optimal weight: 3.9990 chunk 306 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS B 362 ASN ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1073 GLN ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1121 ASN C1121 ASN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 994 GLN J 37 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.211599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.150924 restraints weight = 47915.468| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.61 r_work: 0.3475 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 32913 Z= 0.112 Angle : 0.605 12.948 44902 Z= 0.294 Chirality : 0.045 0.398 5201 Planarity : 0.004 0.055 5668 Dihedral : 6.222 109.357 5836 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.85 % Rotamer: Outliers : 2.37 % Allowed : 17.87 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.44 (0.13), residues: 3924 helix: 0.57 (0.21), residues: 702 sheet: -0.02 (0.18), residues: 816 loop : -1.87 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 187 TYR 0.025 0.001 TYR L 49 PHE 0.022 0.001 PHE C 92 TRP 0.028 0.001 TRP D 149 HIS 0.003 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00262 (32793) covalent geometry : angle 0.58598 (44590) SS BOND : bond 0.00272 ( 45) SS BOND : angle 1.39661 ( 90) hydrogen bonds : bond 0.03416 ( 932) hydrogen bonds : angle 5.48212 ( 2535) Misc. bond : bond 0.00004 ( 1) link_BETA1-4 : bond 0.00480 ( 25) link_BETA1-4 : angle 1.67556 ( 75) link_NAG-ASN : bond 0.00459 ( 49) link_NAG-ASN : angle 2.27331 ( 147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 160 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 22 THR cc_start: 0.5725 (OUTLIER) cc_final: 0.5162 (m) REVERT: B 360 ILE cc_start: 0.8322 (mt) cc_final: 0.8052 (mm) REVERT: B 520 LEU cc_start: 0.5389 (OUTLIER) cc_final: 0.4526 (tp) REVERT: B 756 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9021 (mp) REVERT: B 857 PHE cc_start: 0.7025 (m-80) cc_final: 0.6810 (m-80) REVERT: B 877 SER cc_start: 0.9294 (OUTLIER) cc_final: 0.9063 (p) REVERT: B 1103 HIS cc_start: 0.7807 (OUTLIER) cc_final: 0.6833 (p90) REVERT: C 117 LEU cc_start: 0.7260 (mt) cc_final: 0.6668 (tp) REVERT: C 197 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7349 (t80) REVERT: C 570 ASP cc_start: 0.8008 (p0) cc_final: 0.7645 (p0) REVERT: C 677 GLN cc_start: 0.7832 (mm110) cc_final: 0.7426 (mm-40) REVERT: C 978 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8318 (m) REVERT: C 1052 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8337 (ptp) REVERT: D 54 LEU cc_start: 0.8859 (mt) cc_final: 0.8536 (mp) REVERT: D 549 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7243 (mmmt) REVERT: G 81 MET cc_start: -0.0324 (tpp) cc_final: -0.0853 (ttt) REVERT: I 48 MET cc_start: 0.1808 (OUTLIER) cc_final: 0.1249 (mmm) outliers start: 82 outliers final: 42 residues processed: 227 average time/residue: 0.5064 time to fit residues: 144.0933 Evaluate side-chains 198 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1103 HIS Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 952 ASP Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain I residue 48 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 327 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 121 optimal weight: 0.0670 chunk 238 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 363 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 358 optimal weight: 50.0000 chunk 118 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS B 362 ASN B1073 GLN ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 994 GLN J 37 GLN I 31 ASN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.208782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.150278 restraints weight = 47493.183| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.66 r_work: 0.3418 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 32913 Z= 0.191 Angle : 0.660 13.156 44902 Z= 0.323 Chirality : 0.048 0.408 5201 Planarity : 0.004 0.054 5668 Dihedral : 6.349 109.951 5836 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.19 % Favored : 93.73 % Rotamer: Outliers : 2.61 % Allowed : 18.13 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.51 (0.13), residues: 3924 helix: 0.42 (0.21), residues: 709 sheet: -0.02 (0.18), residues: 811 loop : -1.91 (0.12), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 44 TYR 0.020 0.001 TYR D 267 PHE 0.031 0.002 PHE C 106 TRP 0.031 0.001 TRP D 149 HIS 0.005 0.001 HIS C1050 Details of bonding type rmsd covalent geometry : bond 0.00465 (32793) covalent geometry : angle 0.64011 (44590) SS BOND : bond 0.00415 ( 45) SS BOND : angle 1.75132 ( 90) hydrogen bonds : bond 0.04048 ( 932) hydrogen bonds : angle 5.64778 ( 2535) Misc. bond : bond 0.00028 ( 1) link_BETA1-4 : bond 0.00460 ( 25) link_BETA1-4 : angle 1.69386 ( 75) link_NAG-ASN : bond 0.00431 ( 49) link_NAG-ASN : angle 2.33841 ( 147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 150 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 22 THR cc_start: 0.5783 (OUTLIER) cc_final: 0.5206 (m) REVERT: B 360 ILE cc_start: 0.8310 (mt) cc_final: 0.8023 (mm) REVERT: B 520 LEU cc_start: 0.5342 (OUTLIER) cc_final: 0.4459 (tp) REVERT: B 756 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9002 (mp) REVERT: B 1103 HIS cc_start: 0.8003 (OUTLIER) cc_final: 0.7127 (p90) REVERT: C 117 LEU cc_start: 0.7267 (mt) cc_final: 0.6869 (tp) REVERT: C 197 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7320 (t80) REVERT: C 328 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7914 (pt) REVERT: C 570 ASP cc_start: 0.8090 (p0) cc_final: 0.7712 (p0) REVERT: C 978 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8309 (m) REVERT: D 193 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8124 (m-40) REVERT: D 241 LEU cc_start: 0.7297 (mp) cc_final: 0.7091 (mp) REVERT: D 316 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: D 549 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7305 (mmmt) REVERT: G 48 MET cc_start: 0.4480 (ppp) cc_final: 0.1852 (ptp) REVERT: G 81 MET cc_start: -0.0149 (tpp) cc_final: -0.0696 (ttt) REVERT: I 48 MET cc_start: 0.1870 (OUTLIER) cc_final: 0.1247 (mmm) outliers start: 90 outliers final: 57 residues processed: 225 average time/residue: 0.4667 time to fit residues: 133.9730 Evaluate side-chains 209 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 141 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain B residue 1103 HIS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain C residue 1108 GLN Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 316 GLN Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 81 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 345 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 185 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 192 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 chunk 314 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 179 optimal weight: 0.3980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 ASN B1073 GLN ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1121 ASN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 994 GLN J 37 GLN I 31 ASN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.210112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.155397 restraints weight = 47307.111| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.62 r_work: 0.3442 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 32913 Z= 0.125 Angle : 0.621 13.125 44902 Z= 0.302 Chirality : 0.046 0.396 5201 Planarity : 0.004 0.055 5668 Dihedral : 6.113 110.430 5836 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.44 % Rotamer: Outliers : 2.06 % Allowed : 18.80 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.37 (0.13), residues: 3924 helix: 0.63 (0.21), residues: 699 sheet: 0.04 (0.18), residues: 821 loop : -1.84 (0.12), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 187 TYR 0.027 0.001 TYR B 170 PHE 0.022 0.001 PHE C 92 TRP 0.034 0.001 TRP D 149 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00296 (32793) covalent geometry : angle 0.60249 (44590) SS BOND : bond 0.00291 ( 45) SS BOND : angle 1.40971 ( 90) hydrogen bonds : bond 0.03550 ( 932) hydrogen bonds : angle 5.49513 ( 2535) Misc. bond : bond 0.00007 ( 1) link_BETA1-4 : bond 0.00472 ( 25) link_BETA1-4 : angle 1.62767 ( 75) link_NAG-ASN : bond 0.00429 ( 49) link_NAG-ASN : angle 2.22935 ( 147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 153 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 22 THR cc_start: 0.5670 (OUTLIER) cc_final: 0.5116 (m) REVERT: B 360 ILE cc_start: 0.8297 (mt) cc_final: 0.8016 (mm) REVERT: B 520 LEU cc_start: 0.5422 (OUTLIER) cc_final: 0.4587 (tp) REVERT: B 756 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8985 (mp) REVERT: B 1103 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7063 (p90) REVERT: C 117 LEU cc_start: 0.7223 (mt) cc_final: 0.6798 (tp) REVERT: C 197 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7360 (t80) REVERT: C 328 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7918 (pt) REVERT: C 570 ASP cc_start: 0.8056 (p0) cc_final: 0.7669 (p0) REVERT: C 978 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8270 (m) REVERT: C 1052 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8491 (ptm) REVERT: D 193 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8119 (m-40) REVERT: D 549 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7283 (mmmt) REVERT: G 48 MET cc_start: 0.4499 (ppp) cc_final: 0.1812 (ptp) REVERT: G 58 THR cc_start: 0.1825 (OUTLIER) cc_final: 0.1617 (p) REVERT: G 81 MET cc_start: -0.0174 (tpp) cc_final: -0.0676 (ttt) REVERT: I 48 MET cc_start: 0.1868 (OUTLIER) cc_final: 0.1256 (mmm) outliers start: 71 outliers final: 46 residues processed: 215 average time/residue: 0.4669 time to fit residues: 128.4709 Evaluate side-chains 202 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 144 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1103 HIS Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain C residue 1108 GLN Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1138 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain I residue 48 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 93 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 130 optimal weight: 0.0020 chunk 51 optimal weight: 0.0070 chunk 363 optimal weight: 10.0000 chunk 80 optimal weight: 0.0370 chunk 150 optimal weight: 0.9990 chunk 332 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 272 optimal weight: 4.9990 overall best weight: 0.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 91 GLN B 362 ASN B1073 GLN ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS D 994 GLN J 37 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.211849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.157628 restraints weight = 48004.435| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.75 r_work: 0.3476 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 32913 Z= 0.107 Angle : 0.606 12.676 44902 Z= 0.294 Chirality : 0.045 0.395 5201 Planarity : 0.004 0.055 5668 Dihedral : 5.744 110.314 5835 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 1.71 % Allowed : 19.46 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.13), residues: 3924 helix: 0.83 (0.21), residues: 693 sheet: 0.14 (0.18), residues: 821 loop : -1.79 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 236 TYR 0.022 0.001 TYR C 167 PHE 0.022 0.001 PHE C 92 TRP 0.039 0.001 TRP D 149 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00247 (32793) covalent geometry : angle 0.58916 (44590) SS BOND : bond 0.00229 ( 45) SS BOND : angle 1.14867 ( 90) hydrogen bonds : bond 0.03265 ( 932) hydrogen bonds : angle 5.31771 ( 2535) Misc. bond : bond 0.00001 ( 1) link_BETA1-4 : bond 0.00488 ( 25) link_BETA1-4 : angle 1.56518 ( 75) link_NAG-ASN : bond 0.00439 ( 49) link_NAG-ASN : angle 2.16846 ( 147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 155 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 22 THR cc_start: 0.5590 (OUTLIER) cc_final: 0.5088 (m) REVERT: B 360 ILE cc_start: 0.8372 (mt) cc_final: 0.8101 (mm) REVERT: B 520 LEU cc_start: 0.5416 (OUTLIER) cc_final: 0.4598 (tp) REVERT: B 756 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8972 (mp) REVERT: B 1042 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8730 (p) REVERT: B 1052 MET cc_start: 0.9093 (ptm) cc_final: 0.8748 (ptp) REVERT: B 1103 HIS cc_start: 0.7829 (OUTLIER) cc_final: 0.6971 (p90) REVERT: B 1121 ASN cc_start: 0.7918 (m-40) cc_final: 0.7673 (m110) REVERT: C 197 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7420 (t80) REVERT: C 570 ASP cc_start: 0.8048 (p0) cc_final: 0.7690 (p0) REVERT: C 589 ILE cc_start: 0.8619 (pt) cc_final: 0.8288 (mp) REVERT: C 978 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8302 (m) REVERT: C 1052 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8140 (ppp) REVERT: D 549 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7212 (mmmt) REVERT: G 48 MET cc_start: 0.4433 (ppp) cc_final: 0.1674 (ptp) REVERT: I 48 MET cc_start: 0.1884 (OUTLIER) cc_final: 0.1339 (mmm) outliers start: 59 outliers final: 37 residues processed: 201 average time/residue: 0.4534 time to fit residues: 117.1853 Evaluate side-chains 196 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1103 HIS Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 952 ASP Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 994 GLN Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 81 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 44 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 351 optimal weight: 40.0000 chunk 97 optimal weight: 0.7980 chunk 177 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 367 optimal weight: 20.0000 chunk 375 optimal weight: 30.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 ASN B1073 GLN ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS D 994 GLN J 37 GLN ** K 55 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 = 0.4604 r_free = 0.4604 target = 0.211507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.155873 restraints weight = 47678.201| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.69 r_work: 0.3479 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.324 32913 Z= 0.211 Angle : 0.810 61.599 44902 Z= 0.416 Chirality : 0.047 0.629 5201 Planarity : 0.004 0.086 5668 Dihedral : 5.749 110.254 5835 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.38 % Favored : 94.57 % Rotamer: Outliers : 1.68 % Allowed : 19.66 % Favored : 78.66 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.13), residues: 3924 helix: 0.81 (0.21), residues: 690 sheet: 0.15 (0.18), residues: 821 loop : -1.79 (0.12), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 236 TYR 0.017 0.001 TYR C1140 PHE 0.018 0.001 PHE C 106 TRP 0.033 0.001 TRP D 149 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00451 (32793) covalent geometry : angle 0.79867 (44590) SS BOND : bond 0.00274 ( 45) SS BOND : angle 1.17172 ( 90) hydrogen bonds : bond 0.03393 ( 932) hydrogen bonds : angle 5.33079 ( 2535) Misc. bond : bond 0.00018 ( 1) link_BETA1-4 : bond 0.00490 ( 25) link_BETA1-4 : angle 1.56886 ( 75) link_NAG-ASN : bond 0.00437 ( 49) link_NAG-ASN : angle 2.16681 ( 147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13217.89 seconds wall clock time: 225 minutes 28.23 seconds (13528.23 seconds total)