Starting phenix.real_space_refine on Sat Jul 4 09:08:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yvn_39609/07_2026/8yvn_39609.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yvn_39609/07_2026/8yvn_39609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yvn_39609/07_2026/8yvn_39609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yvn_39609/07_2026/8yvn_39609.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yvn_39609/07_2026/8yvn_39609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yvn_39609/07_2026/8yvn_39609.map" } resolution = 2.8 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= 0.000 sd= 0.089 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 120 5.16 5 C 12340 2.51 5 N 3368 2.21 5 O 4048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19880 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2990 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "B" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2990 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "C" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2990 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "D" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2990 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "E" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "F" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "G" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "I" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "J" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "K" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "U" 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.14, per 1000 atoms: 0.21 Number of scatterers: 19880 At special positions: 0 Unit cell: (125.681, 125.681, 98.8264, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 120 16.00 O 4048 8.00 N 3368 7.00 C 12340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.02 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.02 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.01 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.02 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.02 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.01 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.02 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 193 " distance=2.02 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.01 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.02 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.02 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.02 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=2.02 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.01 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.02 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.02 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN T 4 " - " MAN T 5 " " MAN X 4 " - " MAN X 5 " " MAN b 4 " - " MAN b 5 " ALPHA1-3 " BMA P 3 " - " MAN P 4 " " MAN P 6 " - " MAN P 7 " " BMA T 3 " - " MAN T 4 " " MAN T 6 " - " MAN T 7 " " BMA X 3 " - " MAN X 4 " " MAN X 6 " - " MAN X 7 " " BMA b 3 " - " MAN b 4 " " MAN b 6 " - " MAN b 7 " ALPHA1-6 " BMA P 3 " - " MAN P 6 " " BMA T 3 " - " MAN T 6 " " BMA X 3 " - " MAN X 6 " " BMA b 3 " - " MAN b 6 " BETA1-4 " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " NAG-ASN " NAG A 501 " - " ASN A 86 " " NAG A 502 " - " ASN A 234 " " NAG B 501 " - " ASN B 86 " " NAG B 502 " - " ASN B 234 " " NAG C 501 " - " ASN C 86 " " NAG C 502 " - " ASN C 234 " " NAG D 501 " - " ASN D 86 " " NAG D 502 " - " ASN D 234 " " NAG M 1 " - " ASN A 146 " " NAG N 1 " - " ASN A 367 " " NAG O 1 " - " ASN A 329 " " NAG P 1 " - " ASN A 200 " " NAG Q 1 " - " ASN B 146 " " NAG R 1 " - " ASN B 367 " " NAG S 1 " - " ASN B 329 " " NAG T 1 " - " ASN B 200 " " NAG U 1 " - " ASN C 146 " " NAG V 1 " - " ASN C 367 " " NAG W 1 " - " ASN C 329 " " NAG X 1 " - " ASN C 200 " " NAG Y 1 " - " ASN D 146 " " NAG Z 1 " - " ASN D 367 " " NAG a 1 " - " ASN D 329 " " NAG b 1 " - " ASN D 200 " Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 765.4 milliseconds 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4432 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 44 sheets defined 3.8% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.579A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 329 through 333 removed outlier: 3.795A pdb=" N SER A 333 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.579A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.578A pdb=" N ALA C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 329 through 333 removed outlier: 3.626A pdb=" N SER C 333 " --> pdb=" O ASP C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.579A pdb=" N ALA D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 329 through 333 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.834A pdb=" N PHE I 84 " --> pdb=" O PRO I 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.788A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.841A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 158 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS A 172 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.652A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.786A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR A 252 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N THR A 267 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE A 254 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE A 256 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.588A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.654A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP A 402 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N GLU A 375 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 10.661A pdb=" N ARG A 400 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 11.248A pdb=" N PHE A 377 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 13.273A pdb=" N VAL A 398 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 16.276A pdb=" N VAL A 379 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 16.272A pdb=" N VAL A 396 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 102 removed outlier: 3.788A pdb=" N GLY B 96 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 445 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.841A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.651A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.785A pdb=" N VAL B 231 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR B 252 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N THR B 267 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE B 254 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR B 265 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE B 256 " --> pdb=" O VAL B 263 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.588A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.653A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY B 363 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP B 402 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N GLU B 375 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N ARG B 400 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 11.240A pdb=" N PHE B 377 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 13.271A pdb=" N VAL B 398 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 16.276A pdb=" N VAL B 379 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 16.273A pdb=" N VAL B 396 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 102 removed outlier: 3.790A pdb=" N GLY C 96 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL C 445 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LYS C 102 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ARG C 420 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.842A pdb=" N TRP C 115 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR C 138 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLN C 136 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU C 158 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS C 172 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 179 through 184 removed outlier: 6.652A pdb=" N TYR C 207 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 231 through 233 removed outlier: 3.785A pdb=" N VAL C 231 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR C 252 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N THR C 267 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE C 254 " --> pdb=" O THR C 265 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR C 265 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE C 256 " --> pdb=" O VAL C 263 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 276 through 283 removed outlier: 5.588A pdb=" N GLU C 277 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG C 292 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 352 through 356 removed outlier: 4.654A pdb=" N TRP C 352 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY C 363 " --> pdb=" O TRP C 352 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP C 402 " --> pdb=" O GLY C 373 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N GLU C 375 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N ARG C 400 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 11.342A pdb=" N PHE C 377 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 13.208A pdb=" N VAL C 398 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 16.276A pdb=" N VAL C 379 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 16.274A pdb=" N VAL C 396 " --> pdb=" O VAL C 379 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 96 through 102 removed outlier: 3.788A pdb=" N GLY D 96 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL D 445 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.841A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU D 158 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS D 172 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 179 through 184 removed outlier: 6.652A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 231 through 233 removed outlier: 3.785A pdb=" N VAL D 231 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR D 252 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N THR D 267 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE D 254 " --> pdb=" O THR D 265 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR D 265 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE D 256 " --> pdb=" O VAL D 263 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.588A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 352 through 356 removed outlier: 4.653A pdb=" N TRP D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY D 363 " --> pdb=" O TRP D 352 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASP D 402 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N GLU D 375 " --> pdb=" O ARG D 400 " (cutoff:3.500A) removed outlier: 10.687A pdb=" N ARG D 400 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N PHE D 377 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 13.277A pdb=" N VAL D 398 " --> pdb=" O PHE D 377 " (cutoff:3.500A) removed outlier: 16.276A pdb=" N VAL D 379 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 16.273A pdb=" N VAL D 396 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.752A pdb=" N MET E 34 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N HIS E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR E 59 " --> pdb=" O HIS E 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.761A pdb=" N LEU E 112 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.751A pdb=" N MET F 34 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR F 59 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.762A pdb=" N LEU F 112 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.751A pdb=" N MET G 34 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR G 59 " --> pdb=" O HIS G 50 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.763A pdb=" N LEU G 112 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.448A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR H 59 " --> pdb=" O HIS H 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.763A pdb=" N LEU H 112 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.654A pdb=" N LEU I 13 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU I 34 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AE4, first strand: chain 'J' and resid 11 through 13 removed outlier: 3.785A pdb=" N GLU J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU J 13 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL J 86 " --> pdb=" O HIS J 39 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU J 34 " --> pdb=" O ASP J 50 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASP J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.773A pdb=" N LEU K 34 " --> pdb=" O ASP K 50 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.773A pdb=" N LEU L 34 " --> pdb=" O ASP L 50 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASP L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1671 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: 3.36 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3213 1.30 - 1.43: 5930 1.43 - 1.56: 11020 1.56 - 1.69: 1 1.69 - 1.82: 152 Bond restraints: 20316 Sorted by residual: bond pdb=" N PRO J 8 " pdb=" CD PRO J 8 " ideal model delta sigma weight residual 1.473 1.603 -0.130 1.40e-02 5.10e+03 8.64e+01 bond pdb=" CA SER D 440 " pdb=" CB SER D 440 " ideal model delta sigma weight residual 1.535 1.460 0.075 1.32e-02 5.74e+03 3.24e+01 bond pdb=" CA SER B 388 " pdb=" CB SER B 388 " ideal model delta sigma weight residual 1.530 1.445 0.085 1.50e-02 4.44e+03 3.21e+01 bond pdb=" CA SER A 388 " pdb=" CB SER A 388 " ideal model delta sigma weight residual 1.530 1.446 0.084 1.50e-02 4.44e+03 3.17e+01 bond pdb=" CA SER C 440 " pdb=" CB SER C 440 " ideal model delta sigma weight residual 1.534 1.465 0.070 1.34e-02 5.57e+03 2.70e+01 ... (remaining 20311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 26061 2.81 - 5.63: 1315 5.63 - 8.44: 146 8.44 - 11.25: 39 11.25 - 14.06: 7 Bond angle restraints: 27568 Sorted by residual: angle pdb=" N PRO A 386 " pdb=" CA PRO A 386 " pdb=" C PRO A 386 " ideal model delta sigma weight residual 111.22 97.16 14.06 1.40e+00 5.10e-01 1.01e+02 angle pdb=" N PRO B 386 " pdb=" CA PRO B 386 " pdb=" C PRO B 386 " ideal model delta sigma weight residual 111.22 98.51 12.71 1.40e+00 5.10e-01 8.24e+01 angle pdb=" C THR J 75 " pdb=" CA THR J 75 " pdb=" CB THR J 75 " ideal model delta sigma weight residual 110.14 98.03 12.11 1.54e+00 4.22e-01 6.19e+01 angle pdb=" C THR B 325 " pdb=" CA THR B 325 " pdb=" CB THR B 325 " ideal model delta sigma weight residual 110.17 96.13 14.04 1.97e+00 2.58e-01 5.08e+01 angle pdb=" C GLN K 6 " pdb=" CA GLN K 6 " pdb=" CB GLN K 6 " ideal model delta sigma weight residual 110.26 120.65 -10.39 1.50e+00 4.44e-01 4.80e+01 ... (remaining 27563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 12023 23.14 - 46.29: 636 46.29 - 69.43: 76 69.43 - 92.57: 55 92.57 - 115.72: 34 Dihedral angle restraints: 12824 sinusoidal: 5832 harmonic: 6992 Sorted by residual: dihedral pdb=" CB CYS D 183 " pdb=" SG CYS D 183 " pdb=" SG CYS D 230 " pdb=" CB CYS D 230 " ideal model delta sinusoidal sigma weight residual -86.00 -152.90 66.90 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS C 183 " pdb=" SG CYS C 183 " pdb=" SG CYS C 230 " pdb=" CB CYS C 230 " ideal model delta sinusoidal sigma weight residual -86.00 -152.88 66.88 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS B 183 " pdb=" SG CYS B 183 " pdb=" SG CYS B 230 " pdb=" CB CYS B 230 " ideal model delta sinusoidal sigma weight residual -86.00 -152.86 66.86 1 1.00e+01 1.00e-02 5.83e+01 ... (remaining 12821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.264: 3115 0.264 - 0.528: 63 0.528 - 0.793: 3 0.793 - 1.057: 2 1.057 - 1.321: 1 Chirality restraints: 3184 Sorted by residual: chirality pdb=" C1 MAN P 7 " pdb=" O3 MAN P 6 " pdb=" C2 MAN P 7 " pdb=" O5 MAN P 7 " both_signs ideal model delta sigma weight residual False 2.40 1.08 1.32 2.00e-02 2.50e+03 4.36e+03 chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.39 -1.01 2.00e-02 2.50e+03 2.56e+03 chirality pdb=" C1 MAN X 5 " pdb=" O2 MAN X 4 " pdb=" C2 MAN X 5 " pdb=" O5 MAN X 5 " both_signs ideal model delta sigma weight residual False 2.40 1.54 0.86 2.00e-02 2.50e+03 1.86e+03 ... (remaining 3181 not shown) Planarity restraints: 3484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " -0.291 2.00e-02 2.50e+03 2.52e-01 7.93e+02 pdb=" C7 NAG T 1 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " -0.001 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " 0.430 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " -0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " 0.290 2.00e-02 2.50e+03 2.51e-01 7.88e+02 pdb=" C7 NAG X 1 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " 0.002 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " -0.429 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 1 " 0.248 2.00e-02 2.50e+03 2.14e-01 5.74e+02 pdb=" C7 NAG b 1 " -0.055 2.00e-02 2.50e+03 pdb=" C8 NAG b 1 " -0.015 2.00e-02 2.50e+03 pdb=" N2 NAG b 1 " -0.362 2.00e-02 2.50e+03 pdb=" O7 NAG b 1 " 0.185 2.00e-02 2.50e+03 ... (remaining 3481 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 4 2.10 - 2.80: 5408 2.80 - 3.50: 24769 3.50 - 4.20: 51636 4.20 - 4.90: 91015 Nonbonded interactions: 172832 Sorted by model distance: nonbonded pdb=" NH1 ARG I 24 " pdb=" OD1 ASP I 71 " model vdw 1.397 3.120 nonbonded pdb=" CE1 HIS E 50 " pdb=" CD1 ILE E 58 " model vdw 1.660 3.680 nonbonded pdb=" ND1 HIS E 50 " pdb=" CD1 ILE E 58 " model vdw 1.794 3.540 nonbonded pdb=" CZ ARG I 24 " pdb=" OD1 ASP I 71 " model vdw 1.889 3.270 nonbonded pdb=" O THR J 75 " pdb=" OG1 THR J 75 " model vdw 2.145 3.040 ... (remaining 172827 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'U' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'P' selection = chain 'T' selection = chain 'X' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.810 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:7.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 : 0.010 0.130 20424 Z= 0.603 Angle : 1.393 18.470 27848 Z= 0.828 Chirality : 0.096 1.321 3184 Planarity : 0.014 0.252 3460 Dihedral : 15.770 115.718 8260 Min Nonbonded Distance : 1.397 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.03 % Favored : 94.68 % Rotamer: Outliers : 0.43 % Allowed : 3.65 % Favored : 95.92 % Cbeta Deviations : 1.04 % Peptide Plane: Cis-proline : 13.04 % 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: -1.71 (0.15), residues: 2444 helix: -1.79 (0.71), residues: 24 sheet: -0.49 (0.15), residues: 1028 loop : -1.66 (0.14), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 19 TYR 0.046 0.003 TYR J 87 PHE 0.027 0.003 PHE L 63 TRP 0.019 0.002 TRP B 178 HIS 0.012 0.003 HIS D 264 Details of bonding type rmsd/Z covalent geometry : bond 0.01046 / 0.60 (20316) covalent geometry : angle 1.32725 / 0.82 (27568) SS BOND : bond 0.00771 / 0.50 ( 44) SS BOND : angle 1.70785 / 1.21 ( 88) hydrogen bonds : bond 0.13690 / 9.12 ( 635) hydrogen bonds : angle 7.81877 / 5.38 ( 1671) link_ALPHA1-2 : bond 0.01955 / 0.98 ( 4) link_ALPHA1-2 : angle 4.49426 / 2.32 ( 12) link_ALPHA1-3 : bond 0.02162 / 1.07 ( 8) link_ALPHA1-3 : angle 7.23015 / 3.85 ( 24) link_ALPHA1-6 : bond 0.00872 / 0.45 ( 4) link_ALPHA1-6 : angle 2.21604 / 1.02 ( 12) link_BETA1-4 : bond 0.01284 / 0.84 ( 24) link_BETA1-4 : angle 4.58790 / 3.00 ( 72) link_NAG-ASN : bond 0.01449 / 0.76 ( 24) link_NAG-ASN : angle 5.42160 / 3.46 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 430 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASN cc_start: 0.9005 (t0) cc_final: 0.8710 (t0) REVERT: A 413 GLU cc_start: 0.7107 (tt0) cc_final: 0.6718 (tt0) REVERT: B 141 ASN cc_start: 0.8996 (t0) cc_final: 0.8686 (t0) REVERT: B 390 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8502 (mp) REVERT: C 141 ASN cc_start: 0.9031 (t0) cc_final: 0.8734 (t0) REVERT: C 400 ARG cc_start: 0.7827 (ttp-110) cc_final: 0.7605 (ptp-170) REVERT: C 413 GLU cc_start: 0.7112 (tt0) cc_final: 0.6750 (tt0) REVERT: D 141 ASN cc_start: 0.9123 (t0) cc_final: 0.8854 (t0) REVERT: D 413 GLU cc_start: 0.7106 (tt0) cc_final: 0.6785 (tt0) REVERT: E 56 LEU cc_start: 0.8824 (tp) cc_final: 0.8607 (tp) REVERT: F 13 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7349 (mm-40) REVERT: I 5 THR cc_start: 0.8888 (m) cc_final: 0.8433 (p) REVERT: I 62 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7469 (mtm-85) REVERT: J 4 LEU cc_start: 0.8607 (mt) cc_final: 0.8332 (mt) REVERT: J 5 THR cc_start: 0.8968 (m) cc_final: 0.8561 (p) REVERT: K 5 THR cc_start: 0.8921 (m) cc_final: 0.8525 (p) REVERT: K 62 ARG cc_start: 0.7702 (mtm-85) cc_final: 0.7464 (mtm-85) REVERT: L 5 THR cc_start: 0.8813 (m) cc_final: 0.8348 (p) REVERT: L 62 ARG cc_start: 0.7563 (mtm-85) cc_final: 0.7249 (mtm-85) outliers start: 9 outliers final: 2 residues processed: 436 average time/residue: 0.5012 time to fit residues: 249.0333 Evaluate side-chains 291 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 288 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain L residue 3 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN B 294 ASN B 391 GLN C 294 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN E 35 ASN E 77 ASN F 35 ASN F 77 ASN G 35 ASN H 35 ASN H 77 ASN I 27 GLN I 90 GLN J 90 GLN K 90 GLN L 90 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.095101 restraints weight = 25231.503| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.88 r_work: 0.2925 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20424 Z= 0.146 Angle : 0.745 10.653 27848 Z= 0.356 Chirality : 0.049 0.330 3184 Planarity : 0.005 0.054 3460 Dihedral : 11.515 84.430 3996 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.60 % Favored : 96.36 % Rotamer: Outliers : 2.56 % Allowed : 12.52 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -1.31 (0.16), residues: 2444 helix: -1.62 (0.76), residues: 24 sheet: -0.29 (0.16), residues: 976 loop : -1.29 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 210 TYR 0.016 0.002 TYR F 95 PHE 0.015 0.002 PHE L 72 TRP 0.017 0.001 TRP D 178 HIS 0.006 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (20316) covalent geometry : angle 0.68722 / 0.34 (27568) SS BOND : bond 0.00349 / 0.23 ( 44) SS BOND : angle 1.01702 / 0.70 ( 88) hydrogen bonds : bond 0.03650 / 2.44 ( 635) hydrogen bonds : angle 6.47672 / 4.47 ( 1671) link_ALPHA1-2 : bond 0.00838 / 0.41 ( 4) link_ALPHA1-2 : angle 1.88397 / 0.94 ( 12) link_ALPHA1-3 : bond 0.01617 / 0.78 ( 8) link_ALPHA1-3 : angle 5.52550 / 3.02 ( 24) link_ALPHA1-6 : bond 0.01295 / 0.65 ( 4) link_ALPHA1-6 : angle 1.41893 / 0.74 ( 12) link_BETA1-4 : bond 0.00837 / 0.49 ( 24) link_BETA1-4 : angle 3.47513 / 2.29 ( 72) link_NAG-ASN : bond 0.00571 / 0.30 ( 24) link_NAG-ASN : angle 3.04263 / 1.87 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 269 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.8167 (pttm) cc_final: 0.7907 (pttm) REVERT: A 141 ASN cc_start: 0.9118 (t0) cc_final: 0.8805 (t0) REVERT: A 160 MET cc_start: 0.8955 (ttp) cc_final: 0.8627 (ttt) REVERT: A 387 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6689 (mmtm) REVERT: B 128 LYS cc_start: 0.8135 (pttm) cc_final: 0.7878 (pttm) REVERT: B 141 ASN cc_start: 0.9115 (t0) cc_final: 0.8802 (t0) REVERT: B 160 MET cc_start: 0.8981 (ttp) cc_final: 0.8650 (ttt) REVERT: B 335 SER cc_start: 0.9191 (OUTLIER) cc_final: 0.8873 (m) REVERT: B 368 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: C 128 LYS cc_start: 0.8171 (pttm) cc_final: 0.7926 (pttm) REVERT: C 141 ASN cc_start: 0.9183 (t0) cc_final: 0.8843 (t0) REVERT: C 400 ARG cc_start: 0.8309 (ttp-110) cc_final: 0.7917 (ptp-170) REVERT: D 128 LYS cc_start: 0.8180 (pttm) cc_final: 0.7933 (pttm) REVERT: D 141 ASN cc_start: 0.9212 (t0) cc_final: 0.8919 (t0) REVERT: D 160 MET cc_start: 0.8955 (ttp) cc_final: 0.8628 (ttt) REVERT: D 402 ASP cc_start: 0.8564 (m-30) cc_final: 0.8340 (m-30) REVERT: E 33 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: F 33 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: F 83 MET cc_start: 0.8983 (mtp) cc_final: 0.8688 (mtt) REVERT: G 33 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: H 33 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: I 5 THR cc_start: 0.8430 (m) cc_final: 0.7998 (p) REVERT: I 24 ARG cc_start: 0.7815 (mtp-110) cc_final: 0.7585 (mtp-110) REVERT: J 11 LEU cc_start: 0.7332 (tp) cc_final: 0.6711 (pt) REVERT: K 5 THR cc_start: 0.8409 (m) cc_final: 0.7916 (p) REVERT: K 24 ARG cc_start: 0.8067 (tpp-160) cc_final: 0.7203 (mmm160) REVERT: L 5 THR cc_start: 0.8370 (m) cc_final: 0.7870 (p) outliers start: 54 outliers final: 17 residues processed: 302 average time/residue: 0.5422 time to fit residues: 184.2049 Evaluate side-chains 264 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 17 optimal weight: 2.9990 chunk 96 optimal weight: 0.0170 chunk 68 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 127 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.5024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN B 294 ASN B 441 ASN C 294 ASN C 347 HIS ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN E 35 ASN E 77 ASN F 35 ASN F 77 ASN G 35 ASN H 35 ASN H 77 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.119042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.093157 restraints weight = 25018.356| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.71 r_work: 0.2888 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20424 Z= 0.189 Angle : 0.745 14.534 27848 Z= 0.355 Chirality : 0.050 0.388 3184 Planarity : 0.005 0.049 3460 Dihedral : 9.727 91.100 3992 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 3.08 % Allowed : 15.09 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -1.04 (0.16), residues: 2444 helix: -1.20 (0.88), residues: 24 sheet: -0.10 (0.16), residues: 960 loop : -1.10 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 85 TYR 0.018 0.002 TYR F 95 PHE 0.014 0.002 PHE A 354 TRP 0.017 0.002 TRP A 178 HIS 0.010 0.002 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (20316) covalent geometry : angle 0.68054 / 0.34 (27568) SS BOND : bond 0.00374 / 0.25 ( 44) SS BOND : angle 1.07040 / 0.74 ( 88) hydrogen bonds : bond 0.03796 / 2.52 ( 635) hydrogen bonds : angle 6.26032 / 4.34 ( 1671) link_ALPHA1-2 : bond 0.00721 / 0.36 ( 4) link_ALPHA1-2 : angle 1.72635 / 0.85 ( 12) link_ALPHA1-3 : bond 0.01410 / 0.67 ( 8) link_ALPHA1-3 : angle 5.02568 / 2.75 ( 24) link_ALPHA1-6 : bond 0.00638 / 0.32 ( 4) link_ALPHA1-6 : angle 1.80500 / 0.95 ( 12) link_BETA1-4 : bond 0.00769 / 0.46 ( 24) link_BETA1-4 : angle 3.00665 / 2.00 ( 72) link_NAG-ASN : bond 0.00546 / 0.28 ( 24) link_NAG-ASN : angle 4.14829 / 2.89 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 257 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8392 (mt-10) REVERT: A 141 ASN cc_start: 0.9199 (t0) cc_final: 0.8836 (t0) REVERT: A 160 MET cc_start: 0.8916 (ttp) cc_final: 0.8632 (ttt) REVERT: B 119 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8421 (mt-10) REVERT: B 141 ASN cc_start: 0.9215 (t0) cc_final: 0.8853 (t0) REVERT: B 160 MET cc_start: 0.8952 (ttp) cc_final: 0.8691 (ttt) REVERT: B 307 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8628 (tp) REVERT: B 335 SER cc_start: 0.9165 (OUTLIER) cc_final: 0.8776 (m) REVERT: C 119 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: C 141 ASN cc_start: 0.9217 (t0) cc_final: 0.8855 (t0) REVERT: C 160 MET cc_start: 0.8925 (ttp) cc_final: 0.8667 (ttt) REVERT: C 400 ARG cc_start: 0.8421 (ttp-110) cc_final: 0.8073 (ptp-170) REVERT: D 119 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8420 (mp0) REVERT: D 141 ASN cc_start: 0.9223 (t0) cc_final: 0.8841 (t0) REVERT: D 160 MET cc_start: 0.8928 (ttp) cc_final: 0.8640 (ttt) REVERT: D 368 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: D 441 ASN cc_start: 0.9321 (OUTLIER) cc_final: 0.8989 (p0) REVERT: E 33 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: E 72 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8664 (ptt180) REVERT: F 33 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7704 (mm-30) REVERT: G 33 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7644 (mm-30) REVERT: H 33 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.7761 (mm-30) REVERT: I 5 THR cc_start: 0.8636 (m) cc_final: 0.8330 (p) REVERT: K 5 THR cc_start: 0.8687 (m) cc_final: 0.8354 (p) REVERT: K 24 ARG cc_start: 0.8129 (tpp-160) cc_final: 0.7407 (mmm160) REVERT: K 62 ARG cc_start: 0.7632 (mtm-85) cc_final: 0.7372 (mtm-85) REVERT: K 73 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8461 (p) REVERT: L 62 ARG cc_start: 0.7665 (mtm-85) cc_final: 0.7384 (mtm-85) outliers start: 65 outliers final: 21 residues processed: 292 average time/residue: 0.5579 time to fit residues: 184.3809 Evaluate side-chains 277 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 415 LYS Chi-restraints excluded: chain D residue 441 ASN Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 150 optimal weight: 0.9990 chunk 217 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN E 35 ASN F 35 ASN G 35 ASN H 35 ASN H 39 GLN H 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.093494 restraints weight = 25065.974| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.72 r_work: 0.2889 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20424 Z= 0.170 Angle : 0.697 15.152 27848 Z= 0.335 Chirality : 0.047 0.273 3184 Planarity : 0.004 0.046 3460 Dihedral : 8.853 94.904 3992 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 2.85 % Allowed : 16.94 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.16), residues: 2444 helix: -0.99 (0.93), residues: 24 sheet: 0.16 (0.16), residues: 940 loop : -1.06 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 292 TYR 0.013 0.002 TYR A 121 PHE 0.013 0.002 PHE D 410 TRP 0.018 0.001 TRP A 178 HIS 0.008 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (20316) covalent geometry : angle 0.63903 / 0.32 (27568) SS BOND : bond 0.00320 / 0.21 ( 44) SS BOND : angle 0.94001 / 0.65 ( 88) hydrogen bonds : bond 0.03552 / 2.35 ( 635) hydrogen bonds : angle 6.12284 / 4.24 ( 1671) link_ALPHA1-2 : bond 0.00617 / 0.31 ( 4) link_ALPHA1-2 : angle 1.84513 / 0.93 ( 12) link_ALPHA1-3 : bond 0.01351 / 0.64 ( 8) link_ALPHA1-3 : angle 4.64740 / 2.55 ( 24) link_ALPHA1-6 : bond 0.00763 / 0.39 ( 4) link_ALPHA1-6 : angle 1.60539 / 0.85 ( 12) link_BETA1-4 : bond 0.00680 / 0.42 ( 24) link_BETA1-4 : angle 2.86058 / 1.89 ( 72) link_NAG-ASN : bond 0.00385 / 0.19 ( 24) link_NAG-ASN : angle 3.76972 / 2.57 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 246 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8407 (mp0) REVERT: A 141 ASN cc_start: 0.9191 (t0) cc_final: 0.8822 (t0) REVERT: A 160 MET cc_start: 0.8921 (ttp) cc_final: 0.8634 (ttt) REVERT: A 430 ARG cc_start: 0.7984 (tpp-160) cc_final: 0.7643 (mmt180) REVERT: B 119 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: B 141 ASN cc_start: 0.9207 (t0) cc_final: 0.8841 (t0) REVERT: B 160 MET cc_start: 0.8957 (ttp) cc_final: 0.8684 (ttt) REVERT: B 335 SER cc_start: 0.9155 (OUTLIER) cc_final: 0.8736 (m) REVERT: B 430 ARG cc_start: 0.8044 (tpp-160) cc_final: 0.7723 (mmt180) REVERT: C 119 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: C 141 ASN cc_start: 0.9189 (t0) cc_final: 0.8816 (t0) REVERT: C 160 MET cc_start: 0.8944 (ttp) cc_final: 0.8672 (ttt) REVERT: C 400 ARG cc_start: 0.8475 (ttp-110) cc_final: 0.8122 (ptp-170) REVERT: C 430 ARG cc_start: 0.7998 (tpp-160) cc_final: 0.7775 (mmt180) REVERT: D 119 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: D 141 ASN cc_start: 0.9211 (t0) cc_final: 0.8853 (t0) REVERT: D 160 MET cc_start: 0.8937 (ttp) cc_final: 0.8650 (ttt) REVERT: D 368 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: D 430 ARG cc_start: 0.7958 (tpp-160) cc_final: 0.7661 (mmt180) REVERT: E 33 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: E 72 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8697 (ptt180) REVERT: F 33 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7668 (mm-30) REVERT: G 33 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: H 33 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7690 (mm-30) REVERT: I 62 ARG cc_start: 0.7541 (mtm-85) cc_final: 0.7137 (ptt180) REVERT: K 5 THR cc_start: 0.8661 (m) cc_final: 0.8383 (p) REVERT: K 62 ARG cc_start: 0.7588 (mtm-85) cc_final: 0.7102 (mtm-85) REVERT: K 73 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8429 (p) outliers start: 60 outliers final: 23 residues processed: 272 average time/residue: 0.5503 time to fit residues: 169.4758 Evaluate side-chains 267 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 117 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN B 294 ASN C 294 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 441 ASN E 35 ASN F 35 ASN G 35 ASN H 35 ASN H 39 GLN I 39 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.115958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.089836 restraints weight = 25497.775| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.83 r_work: 0.2838 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 20424 Z= 0.238 Angle : 0.743 12.371 27848 Z= 0.362 Chirality : 0.049 0.289 3184 Planarity : 0.005 0.043 3460 Dihedral : 8.827 102.013 3992 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 3.18 % Allowed : 17.69 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.16), residues: 2444 helix: -0.95 (0.97), residues: 24 sheet: 0.17 (0.16), residues: 940 loop : -1.03 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 85 TYR 0.019 0.002 TYR H 95 PHE 0.015 0.003 PHE C 410 TRP 0.019 0.002 TRP A 178 HIS 0.010 0.002 HIS G 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.24 (20316) covalent geometry : angle 0.69021 / 0.35 (27568) SS BOND : bond 0.00462 / 0.30 ( 44) SS BOND : angle 1.00053 / 0.68 ( 88) hydrogen bonds : bond 0.03949 / 2.61 ( 635) hydrogen bonds : angle 6.24101 / 4.34 ( 1671) link_ALPHA1-2 : bond 0.00660 / 0.33 ( 4) link_ALPHA1-2 : angle 1.70160 / 0.85 ( 12) link_ALPHA1-3 : bond 0.01555 / 0.74 ( 8) link_ALPHA1-3 : angle 4.54811 / 2.54 ( 24) link_ALPHA1-6 : bond 0.00452 / 0.24 ( 4) link_ALPHA1-6 : angle 1.76057 / 0.93 ( 12) link_BETA1-4 : bond 0.00656 / 0.40 ( 24) link_BETA1-4 : angle 2.88254 / 1.87 ( 72) link_NAG-ASN : bond 0.00539 / 0.27 ( 24) link_NAG-ASN : angle 3.72472 / 2.53 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 242 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8411 (mp0) REVERT: A 141 ASN cc_start: 0.9117 (t0) cc_final: 0.8750 (t0) REVERT: A 160 MET cc_start: 0.9009 (ttp) cc_final: 0.8680 (ttt) REVERT: A 210 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8298 (mpt-90) REVERT: A 368 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: A 430 ARG cc_start: 0.7801 (tpp-160) cc_final: 0.7459 (mmt180) REVERT: B 119 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8411 (mp0) REVERT: B 141 ASN cc_start: 0.9117 (t0) cc_final: 0.8755 (t0) REVERT: B 160 MET cc_start: 0.9043 (ttp) cc_final: 0.8698 (ttt) REVERT: B 210 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8323 (mpt-90) REVERT: B 335 SER cc_start: 0.9129 (OUTLIER) cc_final: 0.8682 (m) REVERT: B 430 ARG cc_start: 0.7824 (tpp-160) cc_final: 0.7507 (mmt180) REVERT: C 119 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8387 (mp0) REVERT: C 141 ASN cc_start: 0.9111 (t0) cc_final: 0.8744 (t0) REVERT: C 160 MET cc_start: 0.9005 (ttp) cc_final: 0.8692 (ttt) REVERT: C 368 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: C 400 ARG cc_start: 0.8476 (ttp-110) cc_final: 0.8252 (ttp-170) REVERT: C 430 ARG cc_start: 0.7804 (tpp-160) cc_final: 0.7479 (mmt180) REVERT: D 119 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: D 141 ASN cc_start: 0.9133 (t0) cc_final: 0.8779 (t0) REVERT: D 160 MET cc_start: 0.9015 (ttp) cc_final: 0.8687 (ttt) REVERT: D 210 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8273 (mpt-90) REVERT: D 368 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: D 430 ARG cc_start: 0.7798 (tpp-160) cc_final: 0.7465 (mmt180) REVERT: E 33 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: E 72 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8583 (ptt180) REVERT: F 33 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.7635 (mm-30) REVERT: G 33 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.7650 (mm-30) REVERT: H 33 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.7604 (mm-30) REVERT: I 62 ARG cc_start: 0.7394 (mtm-85) cc_final: 0.7108 (mtm-85) REVERT: K 5 THR cc_start: 0.8469 (m) cc_final: 0.8152 (p) REVERT: K 62 ARG cc_start: 0.7435 (mtm-85) cc_final: 0.6967 (mtm-85) REVERT: K 73 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8159 (p) outliers start: 67 outliers final: 25 residues processed: 278 average time/residue: 0.5902 time to fit residues: 184.7395 Evaluate side-chains 275 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 415 LYS Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 230 optimal weight: 0.0010 chunk 33 optimal weight: 0.8980 chunk 172 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN B 294 ASN C 294 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 ASN E 35 ASN F 35 ASN G 35 ASN H 35 ASN I 39 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.093450 restraints weight = 24898.443| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.70 r_work: 0.2879 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20424 Z= 0.157 Angle : 0.677 10.525 27848 Z= 0.327 Chirality : 0.047 0.471 3184 Planarity : 0.004 0.043 3460 Dihedral : 8.399 105.286 3992 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 2.37 % Allowed : 19.07 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.16), residues: 2444 helix: -0.89 (0.97), residues: 24 sheet: 0.21 (0.16), residues: 940 loop : -0.96 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 292 TYR 0.013 0.001 TYR C 121 PHE 0.013 0.002 PHE B 422 TRP 0.019 0.001 TRP A 178 HIS 0.007 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (20316) covalent geometry : angle 0.62725 / 0.32 (27568) SS BOND : bond 0.00340 / 0.22 ( 44) SS BOND : angle 0.74370 / 0.51 ( 88) hydrogen bonds : bond 0.03495 / 2.32 ( 635) hydrogen bonds : angle 6.05363 / 4.20 ( 1671) link_ALPHA1-2 : bond 0.00512 / 0.25 ( 4) link_ALPHA1-2 : angle 1.89345 / 0.97 ( 12) link_ALPHA1-3 : bond 0.01381 / 0.67 ( 8) link_ALPHA1-3 : angle 4.23374 / 2.36 ( 24) link_ALPHA1-6 : bond 0.00786 / 0.41 ( 4) link_ALPHA1-6 : angle 1.54515 / 0.82 ( 12) link_BETA1-4 : bond 0.00637 / 0.40 ( 24) link_BETA1-4 : angle 2.64912 / 1.73 ( 72) link_NAG-ASN : bond 0.00520 / 0.25 ( 24) link_NAG-ASN : angle 3.42079 / 2.31 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: A 141 ASN cc_start: 0.9221 (t0) cc_final: 0.8835 (t0) REVERT: A 160 MET cc_start: 0.8950 (ttp) cc_final: 0.8673 (ttt) REVERT: A 368 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: B 119 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: B 141 ASN cc_start: 0.9209 (t0) cc_final: 0.8836 (t0) REVERT: B 160 MET cc_start: 0.8988 (ttp) cc_final: 0.8699 (ttt) REVERT: C 119 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: C 141 ASN cc_start: 0.9219 (t0) cc_final: 0.8831 (t0) REVERT: C 160 MET cc_start: 0.8955 (ttp) cc_final: 0.8686 (ttt) REVERT: C 368 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: D 119 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: D 141 ASN cc_start: 0.9244 (t0) cc_final: 0.8867 (t0) REVERT: D 160 MET cc_start: 0.8954 (ttp) cc_final: 0.8679 (ttt) REVERT: D 210 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8373 (mpt-90) REVERT: D 368 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: E 33 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: F 33 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7665 (mm-30) REVERT: G 33 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7685 (mm-30) REVERT: H 33 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.7685 (mm-30) REVERT: I 62 ARG cc_start: 0.7566 (mtm-85) cc_final: 0.7291 (mtm-85) REVERT: J 73 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8498 (p) REVERT: K 62 ARG cc_start: 0.7614 (mtm-85) cc_final: 0.7187 (mtm-85) REVERT: K 73 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8459 (p) REVERT: K 83 ASP cc_start: 0.8394 (m-30) cc_final: 0.8125 (m-30) REVERT: L 4 LEU cc_start: 0.8582 (mt) cc_final: 0.8378 (mt) outliers start: 50 outliers final: 22 residues processed: 282 average time/residue: 0.5770 time to fit residues: 183.9804 Evaluate side-chains 276 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 224 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN B 441 ASN C 294 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN E 35 ASN F 35 ASN F 39 GLN G 35 ASN H 35 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.093081 restraints weight = 25008.454| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.72 r_work: 0.2887 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20424 Z= 0.173 Angle : 0.684 9.918 27848 Z= 0.331 Chirality : 0.047 0.482 3184 Planarity : 0.004 0.041 3460 Dihedral : 8.297 106.178 3992 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 2.70 % Allowed : 19.69 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.16), residues: 2444 helix: -0.87 (0.98), residues: 24 sheet: 0.22 (0.16), residues: 940 loop : -0.93 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 430 TYR 0.014 0.002 TYR C 121 PHE 0.013 0.002 PHE D 422 TRP 0.018 0.001 TRP A 178 HIS 0.008 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (20316) covalent geometry : angle 0.63649 / 0.32 (27568) SS BOND : bond 0.00335 / 0.22 ( 44) SS BOND : angle 0.92561 / 0.65 ( 88) hydrogen bonds : bond 0.03548 / 2.35 ( 635) hydrogen bonds : angle 6.02069 / 4.17 ( 1671) link_ALPHA1-2 : bond 0.00512 / 0.26 ( 4) link_ALPHA1-2 : angle 1.82722 / 0.93 ( 12) link_ALPHA1-3 : bond 0.01444 / 0.70 ( 8) link_ALPHA1-3 : angle 4.10742 / 2.30 ( 24) link_ALPHA1-6 : bond 0.00752 / 0.39 ( 4) link_ALPHA1-6 : angle 1.54490 / 0.82 ( 12) link_BETA1-4 : bond 0.00628 / 0.39 ( 24) link_BETA1-4 : angle 2.61167 / 1.70 ( 72) link_NAG-ASN : bond 0.00506 / 0.25 ( 24) link_NAG-ASN : angle 3.38302 / 2.28 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8391 (mp0) REVERT: A 141 ASN cc_start: 0.9235 (t0) cc_final: 0.8859 (t0) REVERT: A 160 MET cc_start: 0.8941 (ttp) cc_final: 0.8666 (ttt) REVERT: A 210 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8370 (mpt-90) REVERT: A 368 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: B 119 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8344 (mp0) REVERT: B 141 ASN cc_start: 0.9253 (t0) cc_final: 0.8879 (t0) REVERT: B 160 MET cc_start: 0.8986 (ttp) cc_final: 0.8715 (ttt) REVERT: B 210 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8372 (mpt-90) REVERT: C 119 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: C 141 ASN cc_start: 0.9233 (t0) cc_final: 0.8851 (t0) REVERT: C 160 MET cc_start: 0.8951 (ttp) cc_final: 0.8677 (ttt) REVERT: C 368 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: C 400 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8299 (ptp-170) REVERT: D 119 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8363 (mp0) REVERT: D 141 ASN cc_start: 0.9256 (t0) cc_final: 0.8884 (t0) REVERT: D 160 MET cc_start: 0.8944 (ttp) cc_final: 0.8662 (ttt) REVERT: D 210 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8384 (mpt-90) REVERT: D 368 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: E 33 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: E 72 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8727 (ptt180) REVERT: F 33 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: G 33 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7584 (mm-30) REVERT: H 33 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.7666 (mm-30) REVERT: I 62 ARG cc_start: 0.7566 (mtm-85) cc_final: 0.7325 (mtm-85) REVERT: J 73 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8509 (p) REVERT: K 62 ARG cc_start: 0.7624 (mtm-85) cc_final: 0.7195 (mtm-85) REVERT: K 73 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8469 (p) REVERT: K 83 ASP cc_start: 0.8395 (m-30) cc_final: 0.8152 (m-30) REVERT: L 62 ARG cc_start: 0.7447 (mtm-85) cc_final: 0.7166 (mtm-85) REVERT: L 100 GLN cc_start: 0.7833 (mp10) cc_final: 0.7615 (mp10) outliers start: 57 outliers final: 27 residues processed: 265 average time/residue: 0.5583 time to fit residues: 167.2073 Evaluate side-chains 275 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 203 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN A 441 ASN B 294 ASN B 441 ASN C 294 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN E 35 ASN F 35 ASN F 39 GLN G 35 ASN H 35 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.118752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.093566 restraints weight = 24745.324| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.62 r_work: 0.2877 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20424 Z= 0.201 Angle : 0.701 9.865 27848 Z= 0.339 Chirality : 0.048 0.479 3184 Planarity : 0.004 0.041 3460 Dihedral : 8.316 107.480 3992 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 2.70 % Allowed : 19.73 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.16), residues: 2444 helix: -0.91 (0.99), residues: 24 sheet: 0.20 (0.16), residues: 940 loop : -0.93 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 292 TYR 0.014 0.002 TYR C 121 PHE 0.013 0.002 PHE C 410 TRP 0.018 0.002 TRP A 178 HIS 0.008 0.002 HIS G 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (20316) covalent geometry : angle 0.65396 / 0.33 (27568) SS BOND : bond 0.00362 / 0.23 ( 44) SS BOND : angle 0.92704 / 0.64 ( 88) hydrogen bonds : bond 0.03708 / 2.44 ( 635) hydrogen bonds : angle 6.07088 / 4.21 ( 1671) link_ALPHA1-2 : bond 0.00550 / 0.27 ( 4) link_ALPHA1-2 : angle 1.75174 / 0.89 ( 12) link_ALPHA1-3 : bond 0.01477 / 0.72 ( 8) link_ALPHA1-3 : angle 4.05425 / 2.29 ( 24) link_ALPHA1-6 : bond 0.00679 / 0.35 ( 4) link_ALPHA1-6 : angle 1.59823 / 0.85 ( 12) link_BETA1-4 : bond 0.00613 / 0.38 ( 24) link_BETA1-4 : angle 2.61005 / 1.68 ( 72) link_NAG-ASN : bond 0.00538 / 0.26 ( 24) link_NAG-ASN : angle 3.44665 / 2.31 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 235 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8360 (mp0) REVERT: A 141 ASN cc_start: 0.9204 (t0) cc_final: 0.8825 (t0) REVERT: A 160 MET cc_start: 0.8972 (ttp) cc_final: 0.8697 (ttt) REVERT: A 210 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8360 (mpt-90) REVERT: A 368 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: B 119 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8349 (mp0) REVERT: B 141 ASN cc_start: 0.9221 (t0) cc_final: 0.8844 (t0) REVERT: B 160 MET cc_start: 0.9005 (ttp) cc_final: 0.8708 (ttt) REVERT: B 210 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8362 (mpt-90) REVERT: B 335 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8704 (m) REVERT: C 119 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8381 (mp0) REVERT: C 141 ASN cc_start: 0.9202 (t0) cc_final: 0.8815 (t0) REVERT: C 160 MET cc_start: 0.8982 (ttp) cc_final: 0.8707 (ttt) REVERT: C 368 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: C 400 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8263 (ptp-170) REVERT: D 119 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: D 128 LYS cc_start: 0.8542 (pttm) cc_final: 0.8225 (ptmt) REVERT: D 141 ASN cc_start: 0.9224 (t0) cc_final: 0.8849 (t0) REVERT: D 160 MET cc_start: 0.8972 (ttp) cc_final: 0.8691 (ttt) REVERT: D 210 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8372 (mpt-90) REVERT: D 368 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: E 33 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: F 33 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: G 33 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.7539 (mm-30) REVERT: H 33 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7642 (mm-30) REVERT: H 118 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8650 (t) REVERT: J 73 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8484 (p) REVERT: K 62 ARG cc_start: 0.7576 (mtm-85) cc_final: 0.7124 (mtm-85) REVERT: K 73 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8450 (p) REVERT: K 83 ASP cc_start: 0.8372 (m-30) cc_final: 0.8102 (m-30) outliers start: 57 outliers final: 28 residues processed: 263 average time/residue: 0.5273 time to fit residues: 156.9351 Evaluate side-chains 273 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 45 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 238 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 0.0470 chunk 165 optimal weight: 0.1980 chunk 112 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN A 441 ASN B 294 ASN C 294 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN E 35 ASN F 35 ASN F 39 GLN G 35 ASN H 35 ASN ** K 90 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 = 0.3340 r_free = 0.3340 target = 0.118935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.093151 restraints weight = 24891.374| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.71 r_work: 0.2898 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20424 Z= 0.147 Angle : 0.670 10.281 27848 Z= 0.323 Chirality : 0.046 0.478 3184 Planarity : 0.004 0.041 3460 Dihedral : 8.102 108.644 3992 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 2.47 % Allowed : 20.16 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.16), residues: 2444 helix: -0.80 (0.99), residues: 24 sheet: 0.24 (0.16), residues: 940 loop : -0.89 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 292 TYR 0.013 0.001 TYR D 121 PHE 0.012 0.002 PHE D 422 TRP 0.018 0.001 TRP D 178 HIS 0.006 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (20316) covalent geometry : angle 0.62620 / 0.31 (27568) SS BOND : bond 0.00287 / 0.18 ( 44) SS BOND : angle 0.78650 / 0.54 ( 88) hydrogen bonds : bond 0.03446 / 2.27 ( 635) hydrogen bonds : angle 5.98981 / 4.15 ( 1671) link_ALPHA1-2 : bond 0.00486 / 0.24 ( 4) link_ALPHA1-2 : angle 1.90534 / 0.98 ( 12) link_ALPHA1-3 : bond 0.01441 / 0.71 ( 8) link_ALPHA1-3 : angle 3.89575 / 2.20 ( 24) link_ALPHA1-6 : bond 0.00885 / 0.46 ( 4) link_ALPHA1-6 : angle 1.51634 / 0.80 ( 12) link_BETA1-4 : bond 0.00632 / 0.39 ( 24) link_BETA1-4 : angle 2.45308 / 1.59 ( 72) link_NAG-ASN : bond 0.00455 / 0.22 ( 24) link_NAG-ASN : angle 3.27924 / 2.20 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 245 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8357 (mp0) REVERT: A 141 ASN cc_start: 0.9209 (t0) cc_final: 0.8852 (t0) REVERT: A 160 MET cc_start: 0.8945 (ttp) cc_final: 0.8651 (ttt) REVERT: A 210 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8370 (mpt-90) REVERT: B 119 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8360 (mp0) REVERT: B 141 ASN cc_start: 0.9227 (t0) cc_final: 0.8873 (t0) REVERT: B 160 MET cc_start: 0.8980 (ttp) cc_final: 0.8698 (ttt) REVERT: B 210 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8371 (mpt-90) REVERT: B 335 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8698 (m) REVERT: C 119 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: C 141 ASN cc_start: 0.9204 (t0) cc_final: 0.8839 (t0) REVERT: C 160 MET cc_start: 0.8951 (ttp) cc_final: 0.8687 (ttt) REVERT: C 368 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: C 400 ARG cc_start: 0.8574 (ttp-170) cc_final: 0.8282 (ptp-170) REVERT: D 119 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: D 128 LYS cc_start: 0.8547 (pttm) cc_final: 0.8261 (ptmt) REVERT: D 141 ASN cc_start: 0.9227 (t0) cc_final: 0.8874 (t0) REVERT: D 160 MET cc_start: 0.8941 (ttp) cc_final: 0.8648 (ttt) REVERT: D 210 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8379 (mpt-90) REVERT: D 368 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: E 33 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: E 72 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8732 (ptt180) REVERT: F 33 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.7477 (mm-30) REVERT: G 33 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: G 118 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8676 (t) REVERT: H 33 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.7568 (mm-30) REVERT: H 118 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8694 (t) REVERT: J 73 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8500 (p) REVERT: J 90 GLN cc_start: 0.9279 (tt0) cc_final: 0.8992 (tt0) REVERT: K 62 ARG cc_start: 0.7587 (mtm-85) cc_final: 0.7168 (mtm-85) REVERT: K 73 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8465 (p) REVERT: K 83 ASP cc_start: 0.8381 (m-30) cc_final: 0.8129 (m-30) REVERT: L 4 LEU cc_start: 0.8511 (mt) cc_final: 0.8241 (mt) REVERT: L 62 ARG cc_start: 0.7361 (mtm-85) cc_final: 0.7051 (ptt180) outliers start: 52 outliers final: 25 residues processed: 270 average time/residue: 0.6463 time to fit residues: 196.7678 Evaluate side-chains 281 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 187 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 141 optimal weight: 0.5980 chunk 186 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN B 294 ASN C 294 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN E 35 ASN E 39 GLN F 35 ASN F 39 GLN G 35 ASN H 35 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.120311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.094539 restraints weight = 25055.471| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.71 r_work: 0.2920 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20424 Z= 0.134 Angle : 0.656 9.914 27848 Z= 0.315 Chirality : 0.046 0.478 3184 Planarity : 0.004 0.041 3460 Dihedral : 7.914 108.531 3992 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 2.18 % Allowed : 20.54 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.16), residues: 2444 helix: -0.73 (1.00), residues: 24 sheet: 0.27 (0.17), residues: 940 loop : -0.84 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 292 TYR 0.012 0.001 TYR D 121 PHE 0.012 0.002 PHE A 422 TRP 0.018 0.001 TRP C 178 HIS 0.006 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (20316) covalent geometry : angle 0.61329 / 0.31 (27568) SS BOND : bond 0.00350 / 0.23 ( 44) SS BOND : angle 0.90485 / 0.62 ( 88) hydrogen bonds : bond 0.03331 / 2.20 ( 635) hydrogen bonds : angle 5.91246 / 4.09 ( 1671) link_ALPHA1-2 : bond 0.00437 / 0.22 ( 4) link_ALPHA1-2 : angle 1.90942 / 0.98 ( 12) link_ALPHA1-3 : bond 0.01410 / 0.70 ( 8) link_ALPHA1-3 : angle 3.71589 / 2.10 ( 24) link_ALPHA1-6 : bond 0.00925 / 0.48 ( 4) link_ALPHA1-6 : angle 1.52700 / 0.81 ( 12) link_BETA1-4 : bond 0.00630 / 0.39 ( 24) link_BETA1-4 : angle 2.34851 / 1.53 ( 72) link_NAG-ASN : bond 0.00430 / 0.21 ( 24) link_NAG-ASN : angle 3.17805 / 2.13 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 243 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: A 141 ASN cc_start: 0.9195 (t0) cc_final: 0.8828 (t0) REVERT: A 160 MET cc_start: 0.8934 (ttp) cc_final: 0.8663 (ttt) REVERT: A 210 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8368 (mpt-90) REVERT: B 119 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: B 141 ASN cc_start: 0.9216 (t0) cc_final: 0.8855 (t0) REVERT: B 160 MET cc_start: 0.8973 (ttp) cc_final: 0.8686 (ttt) REVERT: B 210 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8322 (mpt-90) REVERT: B 335 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8676 (m) REVERT: C 119 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8380 (mp0) REVERT: C 141 ASN cc_start: 0.9205 (t0) cc_final: 0.8834 (t0) REVERT: C 160 MET cc_start: 0.8946 (ttp) cc_final: 0.8677 (ttt) REVERT: C 400 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8272 (ptp-170) REVERT: D 119 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: D 128 LYS cc_start: 0.8518 (pttm) cc_final: 0.8228 (ptmt) REVERT: D 141 ASN cc_start: 0.9224 (t0) cc_final: 0.8867 (t0) REVERT: D 160 MET cc_start: 0.8936 (ttp) cc_final: 0.8662 (ttt) REVERT: D 368 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: E 33 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: E 72 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8704 (ptt180) REVERT: F 33 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7423 (mm-30) REVERT: G 33 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: H 33 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: I 105 GLU cc_start: 0.8068 (pt0) cc_final: 0.7524 (pp20) REVERT: J 73 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8485 (p) REVERT: J 90 GLN cc_start: 0.9252 (tt0) cc_final: 0.8922 (tt0) REVERT: K 4 LEU cc_start: 0.8773 (mt) cc_final: 0.8559 (mt) REVERT: K 38 GLN cc_start: 0.8888 (tt0) cc_final: 0.8626 (tt0) REVERT: K 62 ARG cc_start: 0.7537 (mtm-85) cc_final: 0.7136 (mtm-85) REVERT: K 73 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8448 (p) REVERT: K 83 ASP cc_start: 0.8381 (m-30) cc_final: 0.8134 (m-30) REVERT: L 62 ARG cc_start: 0.7440 (mtm-85) cc_final: 0.7104 (ptt180) outliers start: 46 outliers final: 23 residues processed: 268 average time/residue: 0.5816 time to fit residues: 176.8101 Evaluate side-chains 274 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 11 optimal weight: 7.9990 chunk 224 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 220 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 121 optimal weight: 0.1980 chunk 78 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN B 294 ASN C 294 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN E 35 ASN E 39 GLN F 35 ASN F 39 GLN G 35 ASN G 39 GLN H 35 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 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 = 0.3374 r_free = 0.3374 target = 0.121385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.095700 restraints weight = 24962.499| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.71 r_work: 0.2939 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20424 Z= 0.117 Angle : 0.641 12.661 27848 Z= 0.307 Chirality : 0.045 0.475 3184 Planarity : 0.004 0.041 3460 Dihedral : 7.689 108.365 3992 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 1.94 % Allowed : 21.02 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.17), residues: 2444 helix: -0.69 (1.00), residues: 24 sheet: 0.32 (0.17), residues: 940 loop : -0.79 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 292 TYR 0.013 0.001 TYR I 87 PHE 0.012 0.001 PHE D 422 TRP 0.018 0.001 TRP D 178 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (20316) covalent geometry : angle 0.60138 / 0.30 (27568) SS BOND : bond 0.00310 / 0.20 ( 44) SS BOND : angle 0.77177 / 0.53 ( 88) hydrogen bonds : bond 0.03165 / 2.09 ( 635) hydrogen bonds : angle 5.82311 / 4.03 ( 1671) link_ALPHA1-2 : bond 0.00393 / 0.20 ( 4) link_ALPHA1-2 : angle 1.95720 / 1.01 ( 12) link_ALPHA1-3 : bond 0.01400 / 0.70 ( 8) link_ALPHA1-3 : angle 3.53826 / 2.00 ( 24) link_ALPHA1-6 : bond 0.01034 / 0.53 ( 4) link_ALPHA1-6 : angle 1.53481 / 0.81 ( 12) link_BETA1-4 : bond 0.00642 / 0.40 ( 24) link_BETA1-4 : angle 2.21662 / 1.46 ( 72) link_NAG-ASN : bond 0.00396 / 0.20 ( 24) link_NAG-ASN : angle 3.06315 / 2.05 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5398.42 seconds wall clock time: 93 minutes 4.53 seconds (5584.53 seconds total)