Starting phenix.real_space_refine on Sun Aug 24 12:27:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yvn_39609/08_2025/8yvn_39609.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yvn_39609/08_2025/8yvn_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_39609/08_2025/8yvn_39609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yvn_39609/08_2025/8yvn_39609.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yvn_39609/08_2025/8yvn_39609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yvn_39609/08_2025/8yvn_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.12, 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: 1.48 Conformation dependent library (CDL) restraints added in 727.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.73 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: 2.88 Time building geometry restraints manager: 1.91 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 15.510 Find NCS groups from input model: 0.350 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:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 aren 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 covalent geometry : bond 0.01046 (20316) covalent geometry : angle 1.32725 (27568) SS BOND : bond 0.00771 ( 44) SS BOND : angle 1.70785 ( 88) hydrogen bonds : bond 0.13690 ( 635) hydrogen bonds : angle 7.81877 ( 1671) link_ALPHA1-2 : bond 0.01955 ( 4) link_ALPHA1-2 : angle 4.49426 ( 12) link_ALPHA1-3 : bond 0.02162 ( 8) link_ALPHA1-3 : angle 7.23015 ( 24) link_ALPHA1-6 : bond 0.00872 ( 4) link_ALPHA1-6 : angle 2.21604 ( 12) link_BETA1-4 : bond 0.01284 ( 24) link_BETA1-4 : angle 4.58790 ( 72) link_NAG-ASN : bond 0.01449 ( 24) link_NAG-ASN : angle 5.42160 ( 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 : 0.797 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: 0.7111 (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: 0.8432 (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: 0.7564 (mtm-85) cc_final: 0.7249 (mtm-85) outliers start: 9 outliers final: 2 residues processed: 436 average time/residue: 0.6368 time to fit residues: 314.2528 Evaluate side-chains 295 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 292 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3374 r_free = 0.3374 target = 0.121356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.094935 restraints weight = 25169.088| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.88 r_work: 0.2923 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20424 Z= 0.144 Angle : 0.745 10.635 27848 Z= 0.354 Chirality : 0.049 0.324 3184 Planarity : 0.005 0.054 3460 Dihedral : 11.433 83.937 3996 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 2.51 % Allowed : 12.43 % Favored : 85.06 % 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 aren not related in a simple way. whole: -1.30 (0.16), residues: 2444 helix: -1.62 (0.76), residues: 24 sheet: -0.29 (0.16), residues: 976 loop : -1.28 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 210 TYR 0.016 0.002 TYR F 95 PHE 0.016 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 covalent geometry : bond 0.00314 (20316) covalent geometry : angle 0.68665 (27568) SS BOND : bond 0.00344 ( 44) SS BOND : angle 1.02588 ( 88) hydrogen bonds : bond 0.03605 ( 635) hydrogen bonds : angle 6.46738 ( 1671) link_ALPHA1-2 : bond 0.00739 ( 4) link_ALPHA1-2 : angle 1.86752 ( 12) link_ALPHA1-3 : bond 0.01483 ( 8) link_ALPHA1-3 : angle 5.52346 ( 24) link_ALPHA1-6 : bond 0.01333 ( 4) link_ALPHA1-6 : angle 1.43391 ( 12) link_BETA1-4 : bond 0.00852 ( 24) link_BETA1-4 : angle 3.45517 ( 72) link_NAG-ASN : bond 0.00502 ( 24) link_NAG-ASN : angle 3.15821 ( 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 321 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 268 time to evaluate : 0.964 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: 0.7909 (pttm) REVERT: A 141 ASN cc_start: 0.9113 (t0) cc_final: 0.8797 (t0) REVERT: A 160 MET cc_start: 0.8954 (ttp) cc_final: 0.8629 (ttt) REVERT: A 387 LYS cc_start: 0.7035 (OUTLIER) cc_final: 0.6696 (mmtm) REVERT: B 128 LYS cc_start: 0.8153 (pttm) cc_final: 0.7898 (pttm) REVERT: B 141 ASN cc_start: 0.9112 (t0) cc_final: 0.8799 (t0) REVERT: B 160 MET cc_start: 0.8980 (ttp) cc_final: 0.8650 (ttt) REVERT: B 335 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8887 (m) REVERT: B 368 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: C 128 LYS cc_start: 0.8166 (pttm) cc_final: 0.7922 (pttm) REVERT: C 141 ASN cc_start: 0.9183 (t0) cc_final: 0.8842 (t0) REVERT: C 400 ARG cc_start: 0.8314 (ttp-110) cc_final: 0.7923 (ptp-170) REVERT: D 128 LYS cc_start: 0.8172 (pttm) cc_final: 0.7924 (pttm) REVERT: D 141 ASN cc_start: 0.9209 (t0) cc_final: 0.8914 (t0) REVERT: D 160 MET cc_start: 0.8951 (ttp) cc_final: 0.8625 (ttt) REVERT: D 402 ASP cc_start: 0.8573 (m-30) cc_final: 0.8349 (m-30) REVERT: E 33 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: F 33 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: F 83 MET cc_start: 0.8991 (mtp) cc_final: 0.8692 (mtt) REVERT: G 33 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: H 33 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.7654 (mm-30) REVERT: I 5 THR cc_start: 0.8429 (m) cc_final: 0.8003 (p) REVERT: I 24 ARG cc_start: 0.7817 (mtp-110) cc_final: 0.7582 (mtp-110) REVERT: K 5 THR cc_start: 0.8415 (m) cc_final: 0.7926 (p) REVERT: K 24 ARG cc_start: 0.8074 (tpp-160) cc_final: 0.7395 (mtp-110) REVERT: L 5 THR cc_start: 0.8369 (m) cc_final: 0.7876 (p) outliers start: 53 outliers final: 16 residues processed: 300 average time/residue: 0.7151 time to fit residues: 240.1862 Evaluate side-chains 269 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 307 ILE 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 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 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: 0.6980 chunk 68 optimal weight: 0.6980 chunk 202 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 77 ASN F 35 ASN F 77 ASN G 35 ASN H 35 ASN H 77 ASN I 39 HIS ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.090966 restraints weight = 25213.783| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.68 r_work: 0.2872 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20424 Z= 0.234 Angle : 0.772 16.452 27848 Z= 0.370 Chirality : 0.051 0.375 3184 Planarity : 0.005 0.051 3460 Dihedral : 9.993 91.876 3992 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 3.32 % Allowed : 14.23 % Favored : 82.45 % 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 aren not related in a simple way. whole: -1.09 (0.16), residues: 2444 helix: -1.23 (0.89), residues: 24 sheet: -0.15 (0.16), residues: 960 loop : -1.12 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 85 TYR 0.020 0.002 TYR E 95 PHE 0.015 0.003 PHE L 84 TRP 0.017 0.002 TRP A 178 HIS 0.011 0.002 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00549 (20316) covalent geometry : angle 0.71066 (27568) SS BOND : bond 0.00415 ( 44) SS BOND : angle 1.18176 ( 88) hydrogen bonds : bond 0.04024 ( 635) hydrogen bonds : angle 6.40136 ( 1671) link_ALPHA1-2 : bond 0.00778 ( 4) link_ALPHA1-2 : angle 1.67551 ( 12) link_ALPHA1-3 : bond 0.01512 ( 8) link_ALPHA1-3 : angle 5.20371 ( 24) link_ALPHA1-6 : bond 0.00524 ( 4) link_ALPHA1-6 : angle 1.94554 ( 12) link_BETA1-4 : bond 0.00759 ( 24) link_BETA1-4 : angle 3.16164 ( 72) link_NAG-ASN : bond 0.00655 ( 24) link_NAG-ASN : angle 3.91925 ( 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 330 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 260 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8430 (mp0) REVERT: A 128 LYS cc_start: 0.8682 (pttm) cc_final: 0.8443 (pttm) REVERT: A 141 ASN cc_start: 0.9204 (t0) cc_final: 0.8827 (t0) REVERT: A 160 MET cc_start: 0.8904 (ttp) cc_final: 0.8634 (ttt) REVERT: B 119 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8414 (mp0) REVERT: B 128 LYS cc_start: 0.8660 (pttm) cc_final: 0.8418 (pttm) REVERT: B 141 ASN cc_start: 0.9217 (t0) cc_final: 0.8838 (t0) REVERT: B 160 MET cc_start: 0.8937 (ttp) cc_final: 0.8689 (ttt) REVERT: B 335 SER cc_start: 0.9161 (OUTLIER) cc_final: 0.8766 (m) REVERT: B 441 ASN cc_start: 0.9247 (OUTLIER) cc_final: 0.9042 (p0) REVERT: C 119 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8431 (mt-10) REVERT: C 128 LYS cc_start: 0.8671 (pttm) cc_final: 0.8433 (pttm) REVERT: C 141 ASN cc_start: 0.9227 (t0) cc_final: 0.8855 (t0) REVERT: C 160 MET cc_start: 0.8918 (ttp) cc_final: 0.8683 (ttt) REVERT: C 400 ARG cc_start: 0.8496 (ttp-110) cc_final: 0.8174 (ptp-170) REVERT: D 119 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: D 128 LYS cc_start: 0.8689 (pttm) cc_final: 0.8454 (pttm) REVERT: D 141 ASN cc_start: 0.9245 (t0) cc_final: 0.8860 (t0) REVERT: D 160 MET cc_start: 0.8913 (ttp) cc_final: 0.8646 (ttt) REVERT: D 368 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: E 33 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: E 72 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8693 (ptt180) REVERT: F 33 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7717 (mm-30) REVERT: G 33 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.7802 (mm-30) REVERT: H 33 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.7731 (mm-30) REVERT: I 5 THR cc_start: 0.8651 (m) cc_final: 0.8361 (p) REVERT: I 10 THR cc_start: 0.8076 (t) cc_final: 0.7842 (p) REVERT: J 62 ARG cc_start: 0.7503 (mtm-85) cc_final: 0.7289 (mtm-85) REVERT: K 5 THR cc_start: 0.8699 (m) cc_final: 0.8386 (p) REVERT: K 24 ARG cc_start: 0.8141 (tpp-160) cc_final: 0.7460 (mmm160) REVERT: K 62 ARG cc_start: 0.7689 (mtm-85) cc_final: 0.7116 (mtm-85) REVERT: K 73 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8509 (p) REVERT: K 80 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7722 (mm-30) REVERT: L 62 ARG cc_start: 0.7719 (mtm-85) cc_final: 0.7317 (mtm-85) outliers start: 70 outliers final: 27 residues processed: 300 average time/residue: 0.7018 time to fit residues: 236.2145 Evaluate side-chains 282 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 415 LYS 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 387 LYS Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 234 ASN 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 307 ILE 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 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 52 SER 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 K residue 80 GLU 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: 2.9990 chunk 217 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 H 77 ASN I 39 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.117496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.091598 restraints weight = 25222.659| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.71 r_work: 0.2861 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20424 Z= 0.203 Angle : 0.720 14.737 27848 Z= 0.348 Chirality : 0.048 0.271 3184 Planarity : 0.005 0.046 3460 Dihedral : 9.124 98.503 3992 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 3.27 % Allowed : 16.22 % Favored : 80.50 % 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 aren not related in a simple way. whole: -0.96 (0.16), residues: 2444 helix: -0.94 (0.96), residues: 24 sheet: 0.02 (0.16), residues: 952 loop : -1.10 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 292 TYR 0.015 0.002 TYR H 95 PHE 0.014 0.002 PHE B 410 TRP 0.019 0.002 TRP B 178 HIS 0.009 0.002 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00473 (20316) covalent geometry : angle 0.66445 (27568) SS BOND : bond 0.00373 ( 44) SS BOND : angle 1.03336 ( 88) hydrogen bonds : bond 0.03784 ( 635) hydrogen bonds : angle 6.25160 ( 1671) link_ALPHA1-2 : bond 0.00653 ( 4) link_ALPHA1-2 : angle 1.77327 ( 12) link_ALPHA1-3 : bond 0.01437 ( 8) link_ALPHA1-3 : angle 4.83707 ( 24) link_ALPHA1-6 : bond 0.00629 ( 4) link_ALPHA1-6 : angle 1.66300 ( 12) link_BETA1-4 : bond 0.00669 ( 24) link_BETA1-4 : angle 2.98998 ( 72) link_NAG-ASN : bond 0.00451 ( 24) link_NAG-ASN : angle 3.50683 ( 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 335 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 266 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: A 128 LYS cc_start: 0.8608 (pttm) cc_final: 0.8312 (ptmt) REVERT: A 141 ASN cc_start: 0.9192 (t0) cc_final: 0.8829 (t0) REVERT: A 160 MET cc_start: 0.8961 (ttp) cc_final: 0.8672 (ttt) REVERT: A 387 LYS cc_start: 0.7095 (mtmm) cc_final: 0.6649 (mmtm) REVERT: A 430 ARG cc_start: 0.8013 (tpp-160) cc_final: 0.7664 (mmt180) REVERT: B 119 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: B 128 LYS cc_start: 0.8593 (pttm) cc_final: 0.8314 (ptmt) REVERT: B 141 ASN cc_start: 0.9198 (t0) cc_final: 0.8837 (t0) REVERT: B 160 MET cc_start: 0.9000 (ttp) cc_final: 0.8730 (ttt) REVERT: B 335 SER cc_start: 0.9185 (OUTLIER) cc_final: 0.8768 (m) REVERT: B 430 ARG cc_start: 0.8050 (tpp-160) cc_final: 0.7719 (mmt180) REVERT: C 119 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8416 (mp0) REVERT: C 128 LYS cc_start: 0.8600 (pttm) cc_final: 0.8315 (ptmt) REVERT: C 141 ASN cc_start: 0.9199 (t0) cc_final: 0.8840 (t0) REVERT: C 160 MET cc_start: 0.8969 (ttp) cc_final: 0.8708 (ttt) REVERT: C 400 ARG cc_start: 0.8479 (ttp-110) cc_final: 0.8086 (ptp-170) REVERT: C 430 ARG cc_start: 0.8023 (tpp-160) cc_final: 0.7682 (mmt180) REVERT: D 119 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8387 (mp0) REVERT: D 128 LYS cc_start: 0.8642 (pttm) cc_final: 0.8352 (ptmt) REVERT: D 141 ASN cc_start: 0.9213 (t0) cc_final: 0.8834 (t0) REVERT: D 160 MET cc_start: 0.8970 (ttp) cc_final: 0.8690 (ttt) REVERT: D 430 ARG cc_start: 0.8020 (tpp-160) cc_final: 0.7681 (mmt180) REVERT: E 33 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: E 72 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8701 (ptt180) REVERT: F 33 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7662 (mm-30) REVERT: F 115 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.6755 (pp30) REVERT: G 33 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7735 (mm-30) REVERT: H 33 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: I 10 THR cc_start: 0.8111 (t) cc_final: 0.7866 (p) REVERT: J 100 GLN cc_start: 0.7773 (mp10) cc_final: 0.7565 (mp10) REVERT: K 5 THR cc_start: 0.8657 (m) cc_final: 0.8379 (p) REVERT: K 62 ARG cc_start: 0.7579 (mtm-85) cc_final: 0.7061 (mtm-85) REVERT: K 73 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8425 (p) REVERT: K 80 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7608 (mm-30) REVERT: L 62 ARG cc_start: 0.7681 (mtm-85) cc_final: 0.7313 (mtm-85) outliers start: 69 outliers final: 22 residues processed: 292 average time/residue: 0.6786 time to fit residues: 223.2066 Evaluate side-chains 283 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 248 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 390 LEU Chi-restraints excluded: chain B residue 119 GLU 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 234 ASN Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 307 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 115 GLN 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 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 K residue 80 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 117 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 209 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 225 optimal weight: 5.9990 chunk 106 optimal weight: 0.0570 chunk 98 optimal weight: 0.0870 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 E 77 ASN F 35 ASN G 35 ASN H 35 ASN H 39 GLN I 90 GLN J 90 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.094933 restraints weight = 24955.894| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.72 r_work: 0.2937 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20424 Z= 0.115 Angle : 0.638 12.053 27848 Z= 0.307 Chirality : 0.045 0.280 3184 Planarity : 0.004 0.045 3460 Dihedral : 8.141 101.954 3992 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.03 % Favored : 96.93 % Rotamer: Outliers : 2.42 % Allowed : 18.93 % Favored : 78.65 % 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 aren not related in a simple way. whole: -0.63 (0.16), residues: 2444 helix: -0.91 (0.93), residues: 24 sheet: 0.32 (0.16), residues: 964 loop : -0.94 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 118 TYR 0.011 0.001 TYR C 121 PHE 0.012 0.001 PHE C 422 TRP 0.017 0.001 TRP B 178 HIS 0.004 0.001 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00254 (20316) covalent geometry : angle 0.59197 (27568) SS BOND : bond 0.00368 ( 44) SS BOND : angle 0.71434 ( 88) hydrogen bonds : bond 0.03116 ( 635) hydrogen bonds : angle 5.91275 ( 1671) link_ALPHA1-2 : bond 0.00398 ( 4) link_ALPHA1-2 : angle 2.06364 ( 12) link_ALPHA1-3 : bond 0.01284 ( 8) link_ALPHA1-3 : angle 4.19973 ( 24) link_ALPHA1-6 : bond 0.01058 ( 4) link_ALPHA1-6 : angle 1.49781 ( 12) link_BETA1-4 : bond 0.00671 ( 24) link_BETA1-4 : angle 2.60330 ( 72) link_NAG-ASN : bond 0.00265 ( 24) link_NAG-ASN : angle 2.97616 ( 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 319 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 268 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8346 (mp0) REVERT: A 128 LYS cc_start: 0.8533 (pttm) cc_final: 0.8262 (ptmt) REVERT: A 141 ASN cc_start: 0.9229 (t0) cc_final: 0.8836 (t0) REVERT: A 160 MET cc_start: 0.8877 (ttp) cc_final: 0.8630 (ttt) REVERT: A 368 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: B 128 LYS cc_start: 0.8497 (pttm) cc_final: 0.8229 (ptmt) REVERT: B 141 ASN cc_start: 0.9243 (t0) cc_final: 0.8855 (t0) REVERT: B 160 MET cc_start: 0.8922 (ttp) cc_final: 0.8656 (ttt) REVERT: B 335 SER cc_start: 0.9168 (OUTLIER) cc_final: 0.8778 (m) REVERT: C 119 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: C 128 LYS cc_start: 0.8502 (pttm) cc_final: 0.8235 (ptmt) REVERT: C 141 ASN cc_start: 0.9221 (t0) cc_final: 0.8830 (t0) REVERT: C 160 MET cc_start: 0.8894 (ttp) cc_final: 0.8639 (ttt) REVERT: C 368 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: C 400 ARG cc_start: 0.8417 (ttp-110) cc_final: 0.8042 (ptp-170) REVERT: D 141 ASN cc_start: 0.9248 (t0) cc_final: 0.8867 (t0) REVERT: D 160 MET cc_start: 0.8897 (ttp) cc_final: 0.8625 (ttt) REVERT: E 33 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: F 33 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: G 33 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7503 (mm-30) REVERT: H 33 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7628 (mm-30) REVERT: I 62 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.7319 (mtm-85) REVERT: K 5 THR cc_start: 0.8665 (m) cc_final: 0.8459 (p) REVERT: K 73 THR cc_start: 0.8679 (p) cc_final: 0.8449 (p) outliers start: 51 outliers final: 12 residues processed: 296 average time/residue: 0.6782 time to fit residues: 226.2101 Evaluate side-chains 260 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 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 294 ASN Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 390 LEU 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 H residue 33 GLU 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 K residue 29 LEU 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: 2.9990 chunk 33 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 13 GLN G 35 ASN H 35 ASN H 39 GLN I 39 HIS J 90 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.116260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.091028 restraints weight = 25114.634| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.61 r_work: 0.2868 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 20424 Z= 0.300 Angle : 0.784 10.657 27848 Z= 0.381 Chirality : 0.053 0.516 3184 Planarity : 0.005 0.043 3460 Dihedral : 8.801 103.634 3992 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 2.89 % Allowed : 18.79 % Favored : 78.32 % 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 aren not related in a simple way. whole: -0.87 (0.16), residues: 2444 helix: -0.99 (1.00), residues: 24 sheet: 0.07 (0.16), residues: 948 loop : -1.02 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 85 TYR 0.019 0.003 TYR H 95 PHE 0.017 0.003 PHE A 410 TRP 0.018 0.002 TRP A 178 HIS 0.012 0.002 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00710 (20316) covalent geometry : angle 0.73279 (27568) SS BOND : bond 0.00492 ( 44) SS BOND : angle 1.18828 ( 88) hydrogen bonds : bond 0.04209 ( 635) hydrogen bonds : angle 6.28108 ( 1671) link_ALPHA1-2 : bond 0.00659 ( 4) link_ALPHA1-2 : angle 1.59153 ( 12) link_ALPHA1-3 : bond 0.01586 ( 8) link_ALPHA1-3 : angle 4.44660 ( 24) link_ALPHA1-6 : bond 0.00354 ( 4) link_ALPHA1-6 : angle 2.00188 ( 12) link_BETA1-4 : bond 0.00622 ( 24) link_BETA1-4 : angle 2.94258 ( 72) link_NAG-ASN : bond 0.00812 ( 24) link_NAG-ASN : angle 3.75359 ( 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 298 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 237 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8391 (mp0) REVERT: A 128 LYS cc_start: 0.8713 (pttm) cc_final: 0.8463 (ptmt) REVERT: A 141 ASN cc_start: 0.9208 (t0) cc_final: 0.8841 (t0) REVERT: A 160 MET cc_start: 0.8905 (ttp) cc_final: 0.8660 (ttt) REVERT: A 368 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: B 119 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8362 (mp0) REVERT: B 128 LYS cc_start: 0.8702 (pttm) cc_final: 0.8453 (ptmt) REVERT: B 141 ASN cc_start: 0.9193 (t0) cc_final: 0.8850 (t0) REVERT: B 160 MET cc_start: 0.8958 (ttp) cc_final: 0.8707 (ttt) REVERT: B 335 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8733 (m) REVERT: C 119 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: C 128 LYS cc_start: 0.8695 (pttm) cc_final: 0.8451 (ptmt) REVERT: C 141 ASN cc_start: 0.9217 (t0) cc_final: 0.8854 (t0) REVERT: C 160 MET cc_start: 0.8928 (ttp) cc_final: 0.8684 (ttt) REVERT: C 368 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: D 119 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8376 (mp0) REVERT: D 141 ASN cc_start: 0.9227 (t0) cc_final: 0.8864 (t0) REVERT: D 160 MET cc_start: 0.8919 (ttp) cc_final: 0.8669 (ttt) REVERT: E 33 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: E 72 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8800 (ptt180) REVERT: F 33 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.7547 (mm-30) REVERT: G 33 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7658 (mm-30) REVERT: H 33 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7665 (mm-30) REVERT: I 62 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.7514 (mtm-85) REVERT: J 73 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8606 (p) REVERT: K 62 ARG cc_start: 0.7662 (mpp-170) cc_final: 0.7438 (mtm-85) REVERT: K 73 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8570 (p) outliers start: 61 outliers final: 26 residues processed: 271 average time/residue: 0.7060 time to fit residues: 214.3291 Evaluate side-chains 264 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 368 GLU Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 153 THR 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 C residue 119 GLU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 390 LEU 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 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 29 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 90 GLN 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 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 224 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 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 H 39 GLN I 39 HIS J 90 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.093229 restraints weight = 24973.206| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.71 r_work: 0.2884 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2547 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= 0.151 Angle : 0.680 9.925 27848 Z= 0.327 Chirality : 0.048 0.626 3184 Planarity : 0.004 0.042 3460 Dihedral : 8.273 107.365 3992 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.19 % Favored : 96.77 % Rotamer: Outliers : 2.28 % Allowed : 20.07 % Favored : 77.66 % 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 aren not related in a simple way. whole: -0.73 (0.16), residues: 2444 helix: -1.03 (0.96), residues: 24 sheet: 0.21 (0.16), residues: 940 loop : -0.95 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 210 TYR 0.014 0.001 TYR C 121 PHE 0.013 0.002 PHE B 410 TRP 0.019 0.001 TRP A 178 HIS 0.007 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00343 (20316) covalent geometry : angle 0.63218 (27568) SS BOND : bond 0.00315 ( 44) SS BOND : angle 0.78698 ( 88) hydrogen bonds : bond 0.03509 ( 635) hydrogen bonds : angle 6.07261 ( 1671) link_ALPHA1-2 : bond 0.00512 ( 4) link_ALPHA1-2 : angle 1.90341 ( 12) link_ALPHA1-3 : bond 0.01425 ( 8) link_ALPHA1-3 : angle 4.14845 ( 24) link_ALPHA1-6 : bond 0.00817 ( 4) link_ALPHA1-6 : angle 1.54551 ( 12) link_BETA1-4 : bond 0.00639 ( 24) link_BETA1-4 : angle 2.59392 ( 72) link_NAG-ASN : bond 0.00773 ( 24) link_NAG-ASN : angle 3.41171 ( 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 299 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 251 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8411 (mp0) REVERT: A 141 ASN cc_start: 0.9229 (t0) cc_final: 0.8879 (t0) REVERT: A 160 MET cc_start: 0.8951 (ttp) cc_final: 0.8683 (ttt) REVERT: A 210 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8375 (mpt-90) REVERT: A 368 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: B 119 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8356 (mp0) REVERT: B 141 ASN cc_start: 0.9199 (t0) cc_final: 0.8835 (t0) REVERT: B 160 MET cc_start: 0.8983 (ttp) cc_final: 0.8714 (ttt) REVERT: C 119 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8389 (mp0) REVERT: C 141 ASN cc_start: 0.9209 (t0) cc_final: 0.8862 (t0) REVERT: C 160 MET cc_start: 0.8966 (ttp) cc_final: 0.8697 (ttt) REVERT: C 368 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: C 400 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8201 (ptp-170) REVERT: D 119 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: D 141 ASN cc_start: 0.9249 (t0) cc_final: 0.8905 (t0) REVERT: D 160 MET cc_start: 0.8965 (ttp) cc_final: 0.8693 (ttt) REVERT: D 210 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8395 (mpt-90) REVERT: E 33 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: E 72 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8708 (ptt180) REVERT: F 33 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7653 (mm-30) REVERT: F 110 MET cc_start: 0.9248 (mtm) cc_final: 0.8917 (mtt) REVERT: G 33 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7677 (mm-30) REVERT: H 33 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: I 90 GLN cc_start: 0.9231 (tt0) cc_final: 0.8997 (tt0) REVERT: J 73 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8507 (p) REVERT: K 73 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8456 (p) outliers start: 48 outliers final: 20 residues processed: 273 average time/residue: 0.7242 time to fit residues: 220.8245 Evaluate side-chains 274 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 294 ASN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 234 ASN 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 400 ARG 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 294 ASN Chi-restraints excluded: chain D residue 307 ILE 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 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 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 203 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.091413 restraints weight = 25009.818| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.61 r_work: 0.2867 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 20424 Z= 0.263 Angle : 0.752 10.020 27848 Z= 0.365 Chirality : 0.051 0.610 3184 Planarity : 0.005 0.042 3460 Dihedral : 8.564 107.661 3992 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 2.80 % Allowed : 20.16 % 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 aren not related in a simple way. whole: -0.86 (0.16), residues: 2444 helix: -1.04 (0.99), residues: 24 sheet: 0.03 (0.16), residues: 952 loop : -0.97 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 85 TYR 0.016 0.002 TYR D 121 PHE 0.018 0.003 PHE A 410 TRP 0.018 0.002 TRP A 178 HIS 0.011 0.002 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00624 (20316) covalent geometry : angle 0.70327 (27568) SS BOND : bond 0.00438 ( 44) SS BOND : angle 1.05380 ( 88) hydrogen bonds : bond 0.04033 ( 635) hydrogen bonds : angle 6.21978 ( 1671) link_ALPHA1-2 : bond 0.00617 ( 4) link_ALPHA1-2 : angle 1.63255 ( 12) link_ALPHA1-3 : bond 0.01529 ( 8) link_ALPHA1-3 : angle 4.26182 ( 24) link_ALPHA1-6 : bond 0.00523 ( 4) link_ALPHA1-6 : angle 1.72892 ( 12) link_BETA1-4 : bond 0.00616 ( 24) link_BETA1-4 : angle 2.77070 ( 72) link_NAG-ASN : bond 0.00846 ( 24) link_NAG-ASN : angle 3.64952 ( 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 295 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 236 time to evaluate : 0.656 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: 0.8820 (OUTLIER) cc_final: 0.8411 (mp0) REVERT: A 141 ASN cc_start: 0.9198 (t0) cc_final: 0.8852 (t0) REVERT: A 160 MET cc_start: 0.8964 (ttp) cc_final: 0.8703 (ttt) REVERT: A 210 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8258 (mpt-90) REVERT: A 368 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: B 119 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: B 141 ASN cc_start: 0.9189 (t0) cc_final: 0.8825 (t0) REVERT: B 160 MET cc_start: 0.8995 (ttp) cc_final: 0.8724 (ttt) REVERT: B 210 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8265 (mpt-90) REVERT: C 119 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8381 (mp0) REVERT: C 141 ASN cc_start: 0.9189 (t0) cc_final: 0.8848 (t0) REVERT: C 160 MET cc_start: 0.8982 (ttp) cc_final: 0.8717 (ttt) REVERT: C 368 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: C 400 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8282 (ptp-170) REVERT: D 119 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: D 141 ASN cc_start: 0.9212 (t0) cc_final: 0.8873 (t0) REVERT: D 160 MET cc_start: 0.8957 (ttp) cc_final: 0.8692 (ttt) REVERT: D 210 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8274 (mpt-90) REVERT: E 33 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: E 72 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8776 (ptt180) REVERT: F 33 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.7523 (mm-30) REVERT: G 33 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7581 (mm-30) REVERT: H 33 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7641 (mm-30) REVERT: H 62 ASP cc_start: 0.8191 (m-30) cc_final: 0.7989 (m-30) REVERT: I 62 ARG cc_start: 0.7569 (mtm-85) cc_final: 0.7038 (ptt180) REVERT: I 90 GLN cc_start: 0.9255 (tt0) cc_final: 0.9030 (tt0) REVERT: J 73 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8543 (p) REVERT: K 62 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.7212 (mtm-85) REVERT: K 73 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8509 (p) outliers start: 59 outliers final: 21 residues processed: 267 average time/residue: 0.6775 time to fit residues: 202.8792 Evaluate side-chains 270 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 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 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 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 307 ILE 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 14 SER Chi-restraints excluded: chain I residue 29 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 45 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 238 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 89 optimal weight: 0.0870 chunk 165 optimal weight: 0.0870 chunk 112 optimal weight: 0.7980 chunk 230 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 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 ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.119221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.093369 restraints weight = 24800.738| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.71 r_work: 0.2910 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20424 Z= 0.131 Angle : 0.666 10.114 27848 Z= 0.320 Chirality : 0.048 0.619 3184 Planarity : 0.004 0.042 3460 Dihedral : 8.079 109.830 3992 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 2.23 % Allowed : 20.45 % Favored : 77.32 % 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 aren not related in a simple way. whole: -0.64 (0.16), residues: 2444 helix: -0.94 (0.97), residues: 24 sheet: 0.24 (0.17), residues: 940 loop : -0.87 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 292 TYR 0.012 0.001 TYR D 121 PHE 0.015 0.002 PHE C 410 TRP 0.019 0.001 TRP D 178 HIS 0.005 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00289 (20316) covalent geometry : angle 0.62061 (27568) SS BOND : bond 0.00274 ( 44) SS BOND : angle 0.73539 ( 88) hydrogen bonds : bond 0.03336 ( 635) hydrogen bonds : angle 5.97153 ( 1671) link_ALPHA1-2 : bond 0.00450 ( 4) link_ALPHA1-2 : angle 1.98359 ( 12) link_ALPHA1-3 : bond 0.01378 ( 8) link_ALPHA1-3 : angle 3.94156 ( 24) link_ALPHA1-6 : bond 0.00955 ( 4) link_ALPHA1-6 : angle 1.53703 ( 12) link_BETA1-4 : bond 0.00637 ( 24) link_BETA1-4 : angle 2.43482 ( 72) link_NAG-ASN : bond 0.00882 ( 24) link_NAG-ASN : angle 3.34937 ( 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 295 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 248 time to evaluate : 0.796 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 119 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8388 (mp0) REVERT: A 141 ASN cc_start: 0.9187 (t0) cc_final: 0.8831 (t0) REVERT: A 160 MET cc_start: 0.8955 (ttp) cc_final: 0.8679 (ttt) REVERT: A 368 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: B 119 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: B 141 ASN cc_start: 0.9198 (t0) cc_final: 0.8845 (t0) REVERT: B 160 MET cc_start: 0.9002 (ttp) cc_final: 0.8716 (ttt) REVERT: B 210 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8369 (mpt-90) REVERT: C 119 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: C 141 ASN cc_start: 0.9186 (t0) cc_final: 0.8800 (t0) REVERT: C 160 MET cc_start: 0.8982 (ttp) cc_final: 0.8699 (ttt) REVERT: C 368 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: C 400 ARG cc_start: 0.8547 (ttp-170) cc_final: 0.8260 (ptp-170) REVERT: D 119 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8376 (mp0) REVERT: D 141 ASN cc_start: 0.9211 (t0) cc_final: 0.8838 (t0) REVERT: D 160 MET cc_start: 0.8969 (ttp) cc_final: 0.8696 (ttt) REVERT: E 33 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: E 72 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8708 (ptt180) REVERT: E 118 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8696 (t) REVERT: F 33 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7590 (mm-30) REVERT: G 33 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7504 (mm-30) REVERT: H 33 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7588 (mm-30) REVERT: H 62 ASP cc_start: 0.8182 (m-30) cc_final: 0.7971 (m-30) REVERT: I 62 ARG cc_start: 0.7467 (mtm-85) cc_final: 0.6974 (ptt180) REVERT: I 90 GLN cc_start: 0.9209 (tt0) cc_final: 0.8944 (tt0) REVERT: J 73 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8495 (p) REVERT: K 62 ARG cc_start: 0.7426 (mtm-85) cc_final: 0.6824 (mtp180) REVERT: K 73 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8445 (p) REVERT: L 62 ARG cc_start: 0.7453 (mtm-85) cc_final: 0.6990 (ptt180) outliers start: 47 outliers final: 18 residues processed: 274 average time/residue: 0.6018 time to fit residues: 185.4062 Evaluate side-chains 270 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 294 ASN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 153 THR 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 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 368 GLU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 294 ASN 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 I residue 14 SER Chi-restraints excluded: chain I residue 73 THR 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: 4.9990 chunk 80 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 186 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 F 115 GLN G 35 ASN G 39 GLN H 35 ASN ** L 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 = 0.3342 r_free = 0.3342 target = 0.119131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.093259 restraints weight = 25114.310| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.72 r_work: 0.2911 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 20424 Z= 0.218 Angle : 0.999 59.200 27848 Z= 0.568 Chirality : 0.054 1.050 3184 Planarity : 0.005 0.173 3460 Dihedral : 8.072 109.772 3992 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 1.94 % Allowed : 20.78 % Favored : 77.28 % Cbeta Deviations : 0.14 % 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 aren not related in a simple way. whole: -0.64 (0.16), residues: 2444 helix: -0.94 (0.97), residues: 24 sheet: 0.25 (0.17), residues: 940 loop : -0.88 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 292 TYR 0.012 0.001 TYR D 121 PHE 0.015 0.002 PHE C 410 TRP 0.018 0.001 TRP D 178 HIS 0.006 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00473 (20316) covalent geometry : angle 0.95969 (27568) SS BOND : bond 0.00314 ( 44) SS BOND : angle 2.64131 ( 88) hydrogen bonds : bond 0.03342 ( 635) hydrogen bonds : angle 5.97113 ( 1671) link_ALPHA1-2 : bond 0.00501 ( 4) link_ALPHA1-2 : angle 1.97941 ( 12) link_ALPHA1-3 : bond 0.01594 ( 8) link_ALPHA1-3 : angle 4.01424 ( 24) link_ALPHA1-6 : bond 0.00776 ( 4) link_ALPHA1-6 : angle 1.58567 ( 12) link_BETA1-4 : bond 0.00639 ( 24) link_BETA1-4 : angle 2.44619 ( 72) link_NAG-ASN : bond 0.00630 ( 24) link_NAG-ASN : angle 3.49290 ( 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 281 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 240 time to evaluate : 0.920 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 119 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8392 (mp0) REVERT: A 141 ASN cc_start: 0.9191 (t0) cc_final: 0.8810 (t0) REVERT: A 160 MET cc_start: 0.8955 (ttp) cc_final: 0.8679 (ttt) REVERT: A 368 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: B 119 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: B 141 ASN cc_start: 0.9196 (t0) cc_final: 0.8843 (t0) REVERT: B 160 MET cc_start: 0.9002 (ttp) cc_final: 0.8716 (ttt) REVERT: B 210 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8369 (mpt-90) REVERT: B 335 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8712 (m) REVERT: C 119 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8366 (mp0) REVERT: C 141 ASN cc_start: 0.9189 (t0) cc_final: 0.8803 (t0) REVERT: C 160 MET cc_start: 0.8987 (ttp) cc_final: 0.8705 (ttt) REVERT: C 368 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: C 400 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8254 (ptp-170) REVERT: D 119 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: D 141 ASN cc_start: 0.9210 (t0) cc_final: 0.8837 (t0) REVERT: D 160 MET cc_start: 0.8971 (ttp) cc_final: 0.8694 (ttt) REVERT: E 33 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: E 72 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8707 (ptt180) REVERT: E 118 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8692 (t) REVERT: F 33 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7597 (mm-30) REVERT: G 33 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7509 (mm-30) REVERT: H 33 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7585 (mm-30) REVERT: H 62 ASP cc_start: 0.8196 (m-30) cc_final: 0.7979 (m-30) REVERT: I 62 ARG cc_start: 0.7506 (mtm-85) cc_final: 0.7017 (ptt180) REVERT: J 73 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8500 (p) REVERT: K 62 ARG cc_start: 0.7419 (mtm-85) cc_final: 0.6955 (mtp180) REVERT: K 73 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8448 (p) REVERT: L 62 ARG cc_start: 0.7453 (mtm-85) cc_final: 0.6997 (ptt180) outliers start: 41 outliers final: 18 residues processed: 260 average time/residue: 0.6915 time to fit residues: 201.9468 Evaluate side-chains 272 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 307 ILE Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 153 THR 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 368 GLU 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 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 115 GLN 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 I residue 14 SER Chi-restraints excluded: chain I residue 73 THR 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: 2.9990 chunk 60 optimal weight: 3.9990 chunk 220 optimal weight: 0.0020 chunk 84 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 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 = 0.118953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.093040 restraints weight = 25094.897| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.72 r_work: 0.2903 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20424 Z= 0.158 Angle : 0.679 10.178 27848 Z= 0.327 Chirality : 0.050 0.771 3184 Planarity : 0.004 0.042 3460 Dihedral : 8.067 109.184 3992 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 2.04 % Allowed : 20.54 % Favored : 77.42 % 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 aren not related in a simple way. whole: -0.62 (0.16), residues: 2444 helix: -0.88 (0.99), residues: 24 sheet: 0.26 (0.17), residues: 940 loop : -0.86 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 292 TYR 0.013 0.001 TYR C 121 PHE 0.015 0.002 PHE C 410 TRP 0.017 0.001 TRP A 178 HIS 0.007 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00361 (20316) covalent geometry : angle 0.63262 (27568) SS BOND : bond 0.00397 ( 44) SS BOND : angle 1.03739 ( 88) hydrogen bonds : bond 0.03402 ( 635) hydrogen bonds : angle 5.95028 ( 1671) link_ALPHA1-2 : bond 0.00468 ( 4) link_ALPHA1-2 : angle 1.85926 ( 12) link_ALPHA1-3 : bond 0.01407 ( 8) link_ALPHA1-3 : angle 3.86278 ( 24) link_ALPHA1-6 : bond 0.00879 ( 4) link_ALPHA1-6 : angle 1.52808 ( 12) link_BETA1-4 : bond 0.00624 ( 24) link_BETA1-4 : angle 2.45131 ( 72) link_NAG-ASN : bond 0.00801 ( 24) link_NAG-ASN : angle 3.45979 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6413.01 seconds wall clock time: 110 minutes 42.42 seconds (6642.42 seconds total)