Starting phenix.real_space_refine on Thu Feb 5 21:24:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8to7_41438/02_2026/8to7_41438.cif Found real_map, /net/cci-nas-00/data/ceres_data/8to7_41438/02_2026/8to7_41438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8to7_41438/02_2026/8to7_41438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8to7_41438/02_2026/8to7_41438.map" model { file = "/net/cci-nas-00/data/ceres_data/8to7_41438/02_2026/8to7_41438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8to7_41438/02_2026/8to7_41438.cif" } resolution = 3.39 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 12738 2.51 5 N 3423 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20361 Number of models: 1 Model: "" Number of chains: 33 Chain: "E" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "H" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "A" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "G" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "J" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "C" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "K" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" 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: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 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: "F" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.85, per 1000 atoms: 0.24 Number of scatterers: 20361 At special positions: 0 Unit cell: (132.72, 139.02, 136.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4080 8.00 N 3423 7.00 C 12738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 433 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.04 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS A 605 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " " BMA U 3 " - " MAN U 5 " " BMA Z 3 " - " MAN Z 5 " 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 R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG A 701 " - " ASN A 618 " " NAG A 702 " - " ASN A 611 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 611 " " NAG C 701 " - " ASN C 618 " " NAG C 702 " - " ASN C 611 " " NAG D 601 " - " ASN D 133 " " NAG D 602 " - " ASN D 197 " " NAG D 603 " - " ASN D 234 " " NAG D 604 " - " ASN D 276 " " NAG D 605 " - " ASN D 295 " " NAG D 606 " - " ASN D 301 " " NAG D 607 " - " ASN D 332 " " NAG D 608 " - " ASN D 339 " " NAG D 609 " - " ASN D 355 " " NAG D 610 " - " ASN D 363 " " NAG D 611 " - " ASN D 386 " " NAG D 612 " - " ASN D 392 " " NAG D 613 " - " ASN D 448 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 197 " " NAG E 603 " - " ASN E 234 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 295 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 332 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 355 " " NAG E 610 " - " ASN E 363 " " NAG E 611 " - " ASN E 386 " " NAG E 612 " - " ASN E 392 " " NAG E 613 " - " ASN E 448 " " NAG F 601 " - " ASN F 133 " " NAG F 602 " - " ASN F 197 " " NAG F 603 " - " ASN F 234 " " NAG F 604 " - " ASN F 276 " " NAG F 605 " - " ASN F 295 " " NAG F 606 " - " ASN F 301 " " NAG F 607 " - " ASN F 332 " " NAG F 608 " - " ASN F 339 " " NAG F 609 " - " ASN F 355 " " NAG F 610 " - " ASN F 363 " " NAG F 611 " - " ASN F 386 " " NAG F 612 " - " ASN F 392 " " NAG F 613 " - " ASN F 448 " " NAG M 1 " - " ASN E 88 " " NAG N 1 " - " ASN E 156 " " NAG O 1 " - " ASN E 160 " " NAG P 1 " - " ASN E 262 " " NAG Q 1 " - " ASN B 637 " " NAG R 1 " - " ASN D 88 " " NAG S 1 " - " ASN D 156 " " NAG T 1 " - " ASN D 160 " " NAG U 1 " - " ASN D 262 " " NAG V 1 " - " ASN A 637 " " NAG W 1 " - " ASN F 88 " " NAG X 1 " - " ASN F 156 " " NAG Y 1 " - " ASN F 160 " " NAG Z 1 " - " ASN F 262 " " NAG a 1 " - " ASN C 637 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 963.1 milliseconds 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4506 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 42 sheets defined 19.3% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'E' and resid 98 through 115 removed outlier: 4.452A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.743A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 126' Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.057A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.573A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.918A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.529A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 626 removed outlier: 3.570A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.638A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.151A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 116 removed outlier: 4.525A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.566A pdb=" N LEU D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS D 126 " --> pdb=" O THR D 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 126' Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 351 removed outlier: 4.293A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 475 through 481 removed outlier: 3.515A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 4.090A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 596 removed outlier: 3.505A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 615 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 662 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'F' and resid 98 through 115 removed outlier: 4.481A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.885A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.512A pdb=" N THR F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 390 Processing helix chain 'F' and resid 475 through 481 removed outlier: 3.724A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 527 removed outlier: 4.278A pdb=" N GLY C 527 " --> pdb=" O GLY C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 542 removed outlier: 4.168A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 596 removed outlier: 3.619A pdb=" N TRP C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 615 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 636 Processing helix chain 'C' and resid 638 through 664 removed outlier: 3.914A pdb=" N LEU C 663 " --> pdb=" O ASP C 659 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.470A pdb=" N VAL B 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL E 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR B 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N TYR E 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N CYS B 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.082A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.502A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE E 53 " --> pdb=" O CYS E 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.946A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.785A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.938A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.223A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.300A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.430A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.898A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.189A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 359 through 361 Processing sheet with id=AA7, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.189A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.898A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.430A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.300A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.223A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 413 through 420 removed outlier: 3.725A pdb=" N PHE E 383 " --> pdb=" O PHE E 376 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.571A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.511A pdb=" N PHE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.531A pdb=" N LEU H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR H 35 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP H 35A" --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ARG H 38 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLY H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.252A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.252A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AB6, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.582A pdb=" N LYS D 487 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 75 through 76 removed outlier: 3.527A pdb=" N PHE D 53 " --> pdb=" O CYS D 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.689A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 169 through 177 removed outlier: 3.757A pdb=" N LYS D 189 " --> pdb=" O CYS D 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.586A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 271 through 273 removed outlier: 3.670A pdb=" N ILE D 443 " --> pdb=" O ARG D 298 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS D 330 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU D 381 " --> pdb=" O CYS D 378 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.603A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.564A pdb=" N GLN G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AC6, first strand: chain 'G' and resid 57 through 59 removed outlier: 3.575A pdb=" N GLY G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL G 89 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 57 through 59 removed outlier: 3.575A pdb=" N GLY G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL G 89 " --> pdb=" O GLN G 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.542A pdb=" N ALA J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP J 70 " --> pdb=" O ALA J 67 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.952A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU J 33 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.952A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 494 through 499 removed outlier: 6.174A pdb=" N VAL C 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N VAL F 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR C 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N TYR F 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N CYS C 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.181A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.713A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER F 56 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE F 53 " --> pdb=" O CYS F 218 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 91 through 93 removed outlier: 3.566A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY F 237 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 169 through 177 removed outlier: 3.583A pdb=" N LYS F 189 " --> pdb=" O CYS F 131 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.357A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 259 through 261 removed outlier: 3.736A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE F 376 " --> pdb=" O PHE F 383 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 271 through 273 removed outlier: 3.562A pdb=" N MET F 271 " --> pdb=" O GLN F 287 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE F 359 " --> pdb=" O TRP F 395 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 304 through 312 removed outlier: 3.565A pdb=" N ILE F 309 " --> pdb=" O GLN F 315 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.592A pdb=" N ALA I 88 " --> pdb=" O VAL I 109 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TRP I 35A" --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYR I 50 " --> pdb=" O TRP I 35A" (cutoff:3.500A) removed outlier: 7.287A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY I 44 " --> pdb=" O SER I 40 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.592A pdb=" N ALA I 88 " --> pdb=" O VAL I 109 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG I 96 " --> pdb=" O VAL I 100G" (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL I 100G" --> pdb=" O ARG I 96 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.635A pdb=" N ALA K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.892A pdb=" N ASP K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL K 104 " --> pdb=" O GLY K 84 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU K 33 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 1977 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6396 1.34 - 1.47: 5109 1.47 - 1.59: 9099 1.59 - 1.71: 0 1.71 - 1.84: 156 Bond restraints: 20760 Sorted by residual: bond pdb=" N ILE J 48 " pdb=" CA ILE J 48 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.14e-02 7.69e+03 9.88e+00 bond pdb=" N GLY E 459 " pdb=" CA GLY E 459 " ideal model delta sigma weight residual 1.446 1.476 -0.030 9.50e-03 1.11e+04 9.78e+00 bond pdb=" N ARG F 456 " pdb=" CA ARG F 456 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.15e-02 7.56e+03 9.20e+00 bond pdb=" N VAL E 446 " pdb=" CA VAL E 446 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.20e-02 6.94e+03 9.10e+00 bond pdb=" N ARG I 94 " pdb=" CA ARG I 94 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.23e-02 6.61e+03 8.84e+00 ... (remaining 20755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 26072 1.98 - 3.95: 1773 3.95 - 5.93: 246 5.93 - 7.91: 66 7.91 - 9.89: 22 Bond angle restraints: 28179 Sorted by residual: angle pdb=" C SER A 615 " pdb=" N ASN A 616 " pdb=" CA ASN A 616 " ideal model delta sigma weight residual 121.54 131.13 -9.59 1.91e+00 2.74e-01 2.52e+01 angle pdb=" N ASN I 32 " pdb=" CA ASN I 32 " pdb=" C ASN I 32 " ideal model delta sigma weight residual 111.11 116.24 -5.13 1.20e+00 6.94e-01 1.82e+01 angle pdb=" C SER C 615 " pdb=" N ASN C 616 " pdb=" CA ASN C 616 " ideal model delta sigma weight residual 121.54 129.54 -8.00 1.91e+00 2.74e-01 1.76e+01 angle pdb=" C TRP E 427 " pdb=" CA TRP E 427 " pdb=" CB TRP E 427 " ideal model delta sigma weight residual 116.34 110.74 5.60 1.40e+00 5.10e-01 1.60e+01 angle pdb=" CA TYR I 34 " pdb=" CB TYR I 34 " pdb=" CG TYR I 34 " ideal model delta sigma weight residual 113.90 121.09 -7.19 1.80e+00 3.09e-01 1.60e+01 ... (remaining 28174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.76: 12685 21.76 - 43.52: 674 43.52 - 65.28: 129 65.28 - 87.04: 77 87.04 - 108.79: 40 Dihedral angle restraints: 13605 sinusoidal: 6600 harmonic: 7005 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -158.64 72.64 1 1.00e+01 1.00e-02 6.74e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual -86.00 -150.46 64.46 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -142.18 56.18 1 1.00e+01 1.00e-02 4.26e+01 ... (remaining 13602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 3373 0.185 - 0.371: 49 0.371 - 0.556: 2 0.556 - 0.742: 1 0.742 - 0.927: 1 Chirality restraints: 3426 Sorted by residual: chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 618 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.15e+01 chirality pdb=" C1 NAG C 702 " pdb=" ND2 ASN C 611 " pdb=" C2 NAG C 702 " pdb=" O5 NAG C 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.82e+00 chirality pdb=" C1 NAG C 701 " pdb=" ND2 ASN C 618 " pdb=" C2 NAG C 701 " pdb=" O5 NAG C 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 3423 not shown) Planarity restraints: 3537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " -0.311 2.00e-02 2.50e+03 2.65e-01 8.80e+02 pdb=" C7 NAG B 702 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " -0.177 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " 0.464 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 363 " 0.040 2.00e-02 2.50e+03 3.82e-02 1.82e+01 pdb=" CG ASN D 363 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN D 363 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN D 363 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG D 610 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 427 " 0.012 2.00e-02 2.50e+03 1.92e-02 9.22e+00 pdb=" CG TRP D 427 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP D 427 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP D 427 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 427 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 427 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 427 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 427 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 427 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 427 " -0.001 2.00e-02 2.50e+03 ... (remaining 3534 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 98 2.57 - 3.15: 15480 3.15 - 3.74: 28926 3.74 - 4.32: 39666 4.32 - 4.90: 67533 Nonbonded interactions: 151703 Sorted by model distance: nonbonded pdb=" O SER B 615 " pdb=" OD1 ASN B 616 " model vdw 1.991 3.040 nonbonded pdb=" O SER B 615 " pdb=" CG ASN B 616 " model vdw 2.130 3.270 nonbonded pdb=" OD2 ASP G 72 " pdb=" NZ LYS G 75 " model vdw 2.316 3.120 nonbonded pdb=" NH1 ARG D 192 " pdb=" O LEU D 193 " model vdw 2.337 3.120 nonbonded pdb=" OG SER D 447 " pdb=" O7 NAG U 1 " model vdw 2.350 3.040 ... (remaining 151698 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 36.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.070 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.340 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20892 Z= 0.334 Angle : 1.123 16.234 28533 Z= 0.583 Chirality : 0.069 0.927 3426 Planarity : 0.006 0.265 3477 Dihedral : 15.433 108.794 8973 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.17), residues: 2394 helix: 1.43 (0.28), residues: 393 sheet: -1.01 (0.19), residues: 699 loop : -0.99 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 308 TYR 0.034 0.002 TYR D 486 PHE 0.018 0.002 PHE E 233 TRP 0.049 0.002 TRP D 427 HIS 0.025 0.002 HIS I 35B Details of bonding type rmsd covalent geometry : bond 0.00628 (20760) covalent geometry : angle 1.09252 (28179) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.30042 ( 84) hydrogen bonds : bond 0.23818 ( 692) hydrogen bonds : angle 8.29025 ( 1977) link_ALPHA1-3 : bond 0.00570 ( 3) link_ALPHA1-3 : angle 1.20891 ( 9) link_ALPHA1-6 : bond 0.00231 ( 3) link_ALPHA1-6 : angle 1.52907 ( 9) link_BETA1-4 : bond 0.00928 ( 24) link_BETA1-4 : angle 2.38653 ( 72) link_NAG-ASN : bond 0.00471 ( 60) link_NAG-ASN : angle 3.13279 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: E 161 MET cc_start: 0.8325 (tpt) cc_final: 0.7947 (tpt) REVERT: E 166 ARG cc_start: 0.4309 (ttt-90) cc_final: 0.3242 (ttt-90) REVERT: E 462 ASN cc_start: 0.7978 (t0) cc_final: 0.7764 (t0) REVERT: E 475 MET cc_start: 0.8805 (mmm) cc_final: 0.8253 (mmp) REVERT: B 625 ASN cc_start: 0.9150 (t0) cc_final: 0.8798 (t0) REVERT: H 46 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7870 (mt-10) REVERT: H 72 ASP cc_start: 0.8409 (t70) cc_final: 0.7541 (t0) REVERT: L 103 ARG cc_start: 0.8030 (ptm160) cc_final: 0.7389 (ptp-110) REVERT: D 475 MET cc_start: 0.8112 (mmm) cc_final: 0.7867 (mmt) REVERT: A 625 ASN cc_start: 0.9038 (t0) cc_final: 0.8606 (t0) REVERT: G 75 LYS cc_start: 0.8336 (ptpp) cc_final: 0.7724 (ptpp) REVERT: G 100 ASP cc_start: 0.8078 (t0) cc_final: 0.7621 (t0) REVERT: G 105 GLN cc_start: 0.8914 (pt0) cc_final: 0.8058 (pt0) REVERT: G 107 LEU cc_start: 0.8324 (tp) cc_final: 0.7964 (tp) REVERT: G 110 THR cc_start: 0.8671 (m) cc_final: 0.8408 (p) REVERT: F 166 ARG cc_start: 0.4144 (tpt170) cc_final: 0.1499 (tmt170) REVERT: F 479 TRP cc_start: 0.8357 (m-10) cc_final: 0.8141 (m-10) REVERT: I 27 ASP cc_start: 0.9190 (t70) cc_final: 0.8947 (t0) REVERT: I 72 ASP cc_start: 0.8739 (t70) cc_final: 0.8332 (t0) REVERT: I 95 GLU cc_start: 0.8059 (pt0) cc_final: 0.7751 (pt0) REVERT: I 100 ILE cc_start: 0.8715 (mm) cc_final: 0.8295 (mm) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1604 time to fit residues: 73.0422 Evaluate side-chains 235 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.0010 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN ** J 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN C 607 ASN C 653 GLN K 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.074147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.057571 restraints weight = 55628.345| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.90 r_work: 0.2795 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20892 Z= 0.115 Angle : 0.639 12.698 28533 Z= 0.312 Chirality : 0.047 0.471 3426 Planarity : 0.004 0.054 3477 Dihedral : 11.010 79.159 4479 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.98 % Allowed : 5.84 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.17), residues: 2394 helix: 1.59 (0.28), residues: 405 sheet: -0.67 (0.18), residues: 783 loop : -0.87 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 588 TYR 0.014 0.001 TYR D 484 PHE 0.011 0.001 PHE D 383 TRP 0.019 0.001 TRP B 571 HIS 0.008 0.001 HIS G 35B Details of bonding type rmsd covalent geometry : bond 0.00245 (20760) covalent geometry : angle 0.59483 (28179) SS BOND : bond 0.00272 ( 42) SS BOND : angle 0.63757 ( 84) hydrogen bonds : bond 0.04412 ( 692) hydrogen bonds : angle 5.99232 ( 1977) link_ALPHA1-3 : bond 0.00933 ( 3) link_ALPHA1-3 : angle 2.42858 ( 9) link_ALPHA1-6 : bond 0.00384 ( 3) link_ALPHA1-6 : angle 1.85053 ( 9) link_BETA1-4 : bond 0.00731 ( 24) link_BETA1-4 : angle 2.11090 ( 72) link_NAG-ASN : bond 0.00400 ( 60) link_NAG-ASN : angle 2.63734 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 253 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: E 161 MET cc_start: 0.8672 (tpt) cc_final: 0.8421 (tpt) REVERT: E 462 ASN cc_start: 0.7992 (t0) cc_final: 0.7778 (t0) REVERT: B 625 ASN cc_start: 0.9078 (t0) cc_final: 0.8509 (t0) REVERT: H 6 GLU cc_start: 0.8584 (mp0) cc_final: 0.8289 (mp0) REVERT: H 16 GLU cc_start: 0.8584 (pm20) cc_final: 0.8361 (pm20) REVERT: H 46 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8224 (mt-10) REVERT: H 105 GLN cc_start: 0.8961 (pt0) cc_final: 0.8708 (pt0) REVERT: L 79 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7213 (mm-30) REVERT: L 103 ARG cc_start: 0.7583 (ptm160) cc_final: 0.7105 (ptp-110) REVERT: A 621 GLU cc_start: 0.8799 (tt0) cc_final: 0.7936 (tm-30) REVERT: A 625 ASN cc_start: 0.9130 (t0) cc_final: 0.8387 (t0) REVERT: G 3 GLN cc_start: 0.8485 (mm110) cc_final: 0.8282 (mm110) REVERT: G 16 GLU cc_start: 0.8180 (pm20) cc_final: 0.7583 (pm20) REVERT: G 72 ASP cc_start: 0.7968 (p0) cc_final: 0.7618 (p0) REVERT: G 100 ASP cc_start: 0.8374 (t0) cc_final: 0.8085 (t0) REVERT: J 79 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7474 (mm-30) REVERT: J 82 ASP cc_start: 0.7826 (m-30) cc_final: 0.7351 (m-30) REVERT: J 100 GLN cc_start: 0.8782 (pm20) cc_final: 0.8488 (pm20) REVERT: F 166 ARG cc_start: 0.4400 (tpt170) cc_final: 0.3372 (tpt170) REVERT: F 475 MET cc_start: 0.8754 (tpp) cc_final: 0.8243 (mmt) REVERT: I 5 GLN cc_start: 0.8491 (tp-100) cc_final: 0.8066 (tp40) REVERT: I 27 ASP cc_start: 0.9287 (t70) cc_final: 0.8949 (t0) REVERT: I 72 ASP cc_start: 0.8699 (t70) cc_final: 0.8382 (t0) REVERT: I 100 ILE cc_start: 0.8810 (mm) cc_final: 0.8360 (mm) REVERT: K 82 ASP cc_start: 0.7657 (m-30) cc_final: 0.7318 (m-30) outliers start: 21 outliers final: 17 residues processed: 266 average time/residue: 0.1578 time to fit residues: 63.6807 Evaluate side-chains 248 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 83 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 183 optimal weight: 6.9990 chunk 169 optimal weight: 0.6980 chunk 225 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN F 352 HIS ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.067957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.049741 restraints weight = 57812.483| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 3.94 r_work: 0.2592 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20892 Z= 0.224 Angle : 0.681 11.721 28533 Z= 0.334 Chirality : 0.048 0.479 3426 Planarity : 0.004 0.048 3477 Dihedral : 8.510 65.652 4479 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.59 % Allowed : 7.20 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.17), residues: 2394 helix: 1.82 (0.28), residues: 396 sheet: -0.54 (0.18), residues: 807 loop : -0.93 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 94 TYR 0.014 0.002 TYR D 484 PHE 0.022 0.002 PHE H 78 TRP 0.023 0.002 TRP F 479 HIS 0.008 0.001 HIS I 35B Details of bonding type rmsd covalent geometry : bond 0.00529 (20760) covalent geometry : angle 0.64259 (28179) SS BOND : bond 0.00282 ( 42) SS BOND : angle 0.82525 ( 84) hydrogen bonds : bond 0.04511 ( 692) hydrogen bonds : angle 5.30884 ( 1977) link_ALPHA1-3 : bond 0.01062 ( 3) link_ALPHA1-3 : angle 1.88217 ( 9) link_ALPHA1-6 : bond 0.00452 ( 3) link_ALPHA1-6 : angle 1.79626 ( 9) link_BETA1-4 : bond 0.00469 ( 24) link_BETA1-4 : angle 1.94757 ( 72) link_NAG-ASN : bond 0.00376 ( 60) link_NAG-ASN : angle 2.59220 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 246 time to evaluate : 0.518 Fit side-chains REVERT: E 434 MET cc_start: 0.8871 (ttp) cc_final: 0.8660 (ttt) REVERT: E 462 ASN cc_start: 0.8036 (t0) cc_final: 0.7776 (t0) REVERT: E 475 MET cc_start: 0.8984 (mmm) cc_final: 0.7672 (mmm) REVERT: B 621 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7927 (tm-30) REVERT: B 625 ASN cc_start: 0.9014 (t0) cc_final: 0.8436 (t0) REVERT: B 632 ASP cc_start: 0.9138 (t0) cc_final: 0.8820 (t0) REVERT: B 657 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8578 (tm-30) REVERT: H 46 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8132 (mt-10) REVERT: H 72 ASP cc_start: 0.8202 (t0) cc_final: 0.7410 (t0) REVERT: H 75 LYS cc_start: 0.9114 (mtmm) cc_final: 0.8869 (mtmm) REVERT: H 100 TYR cc_start: 0.8742 (m-80) cc_final: 0.8245 (m-80) REVERT: H 100 ASP cc_start: 0.8518 (t0) cc_final: 0.8150 (t0) REVERT: L 79 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7654 (mm-30) REVERT: L 103 ARG cc_start: 0.7521 (ptm160) cc_final: 0.7088 (ptp-110) REVERT: A 621 GLU cc_start: 0.9027 (tt0) cc_final: 0.8289 (tm-30) REVERT: A 625 ASN cc_start: 0.9297 (t0) cc_final: 0.8683 (t0) REVERT: G 5 GLN cc_start: 0.8571 (tp-100) cc_final: 0.8176 (tp-100) REVERT: G 16 GLU cc_start: 0.8336 (pm20) cc_final: 0.7718 (pm20) REVERT: G 75 LYS cc_start: 0.8815 (pttm) cc_final: 0.8609 (tptt) REVERT: G 100 ASP cc_start: 0.8768 (t0) cc_final: 0.8338 (t0) REVERT: J 79 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7740 (mm-30) REVERT: J 100 GLN cc_start: 0.8685 (pm20) cc_final: 0.8472 (pm20) REVERT: F 166 ARG cc_start: 0.4543 (tpt170) cc_final: 0.1139 (tmt170) REVERT: C 621 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7935 (tm-30) REVERT: C 659 ASP cc_start: 0.8697 (t0) cc_final: 0.8280 (m-30) REVERT: I 3 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7887 (mm110) REVERT: I 5 GLN cc_start: 0.8469 (tp-100) cc_final: 0.8103 (tp40) REVERT: I 16 GLU cc_start: 0.8315 (pm20) cc_final: 0.7988 (pm20) REVERT: I 27 ASP cc_start: 0.9285 (t70) cc_final: 0.8801 (t70) REVERT: I 72 ASP cc_start: 0.8607 (t70) cc_final: 0.8168 (t0) REVERT: I 100 ILE cc_start: 0.9116 (mm) cc_final: 0.8875 (mm) REVERT: I 100 ASP cc_start: 0.8418 (t0) cc_final: 0.8141 (t70) REVERT: K 24 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7735 (tmm160) outliers start: 34 outliers final: 25 residues processed: 270 average time/residue: 0.1442 time to fit residues: 58.5886 Evaluate side-chains 249 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 1 ASP Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 184 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 199 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN L 100 GLN A 616 ASN C 607 ASN C 653 GLN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.049632 restraints weight = 57505.095| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.93 r_work: 0.2584 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20892 Z= 0.174 Angle : 0.633 11.895 28533 Z= 0.305 Chirality : 0.047 0.564 3426 Planarity : 0.003 0.044 3477 Dihedral : 7.862 59.911 4479 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.66 % Rotamer: Outliers : 1.68 % Allowed : 8.56 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.17), residues: 2394 helix: 1.90 (0.28), residues: 396 sheet: -0.47 (0.18), residues: 819 loop : -0.93 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 476 TYR 0.012 0.001 TYR F 173 PHE 0.013 0.001 PHE D 53 TRP 0.016 0.001 TRP F 479 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00413 (20760) covalent geometry : angle 0.58838 (28179) SS BOND : bond 0.00229 ( 42) SS BOND : angle 0.60924 ( 84) hydrogen bonds : bond 0.03938 ( 692) hydrogen bonds : angle 5.09406 ( 1977) link_ALPHA1-3 : bond 0.01015 ( 3) link_ALPHA1-3 : angle 1.90870 ( 9) link_ALPHA1-6 : bond 0.00676 ( 3) link_ALPHA1-6 : angle 1.78608 ( 9) link_BETA1-4 : bond 0.00479 ( 24) link_BETA1-4 : angle 1.68759 ( 72) link_NAG-ASN : bond 0.00338 ( 60) link_NAG-ASN : angle 2.77773 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 0.731 Fit side-chains REVERT: E 166 ARG cc_start: 0.5133 (ttt-90) cc_final: 0.4026 (ttt-90) REVERT: E 475 MET cc_start: 0.9013 (mmm) cc_final: 0.8149 (mmm) REVERT: B 613 SER cc_start: 0.9547 (m) cc_final: 0.9313 (t) REVERT: B 621 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7788 (tm-30) REVERT: B 625 ASN cc_start: 0.9017 (t0) cc_final: 0.8342 (t0) REVERT: B 632 ASP cc_start: 0.9139 (t0) cc_final: 0.8776 (t0) REVERT: B 657 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8502 (tm-30) REVERT: H 46 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8031 (mt-10) REVERT: H 72 ASP cc_start: 0.8169 (t0) cc_final: 0.7249 (t0) REVERT: H 75 LYS cc_start: 0.9095 (mtmm) cc_final: 0.8666 (mtmm) REVERT: H 100 TYR cc_start: 0.8876 (m-80) cc_final: 0.8396 (m-80) REVERT: H 100 ASP cc_start: 0.8538 (t0) cc_final: 0.8146 (t0) REVERT: L 79 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7713 (mm-30) REVERT: L 81 GLU cc_start: 0.7501 (pp20) cc_final: 0.7263 (pp20) REVERT: L 103 ARG cc_start: 0.7495 (ptm160) cc_final: 0.7069 (ptp-110) REVERT: A 621 GLU cc_start: 0.8999 (tt0) cc_final: 0.8264 (tm-30) REVERT: A 625 ASN cc_start: 0.9270 (t0) cc_final: 0.8622 (t0) REVERT: G 16 GLU cc_start: 0.8346 (pm20) cc_final: 0.7711 (pm20) REVERT: G 27 ASP cc_start: 0.8955 (t0) cc_final: 0.8471 (t0) REVERT: G 72 ASP cc_start: 0.8131 (p0) cc_final: 0.7901 (p0) REVERT: G 100 ASP cc_start: 0.8692 (t0) cc_final: 0.8267 (t0) REVERT: J 79 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7731 (mm-30) REVERT: J 100 GLN cc_start: 0.8711 (pm20) cc_final: 0.8476 (pm20) REVERT: F 166 ARG cc_start: 0.4288 (tpt170) cc_final: 0.1354 (tmt170) REVERT: C 621 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7864 (tm-30) REVERT: C 659 ASP cc_start: 0.8709 (t0) cc_final: 0.8302 (m-30) REVERT: I 3 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7875 (mm-40) REVERT: I 5 GLN cc_start: 0.8467 (tp-100) cc_final: 0.8105 (tp40) REVERT: I 27 ASP cc_start: 0.9286 (t70) cc_final: 0.8948 (t0) REVERT: I 72 ASP cc_start: 0.8630 (t70) cc_final: 0.8183 (t0) REVERT: K 24 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7764 (tmm160) outliers start: 36 outliers final: 27 residues processed: 257 average time/residue: 0.1496 time to fit residues: 58.4190 Evaluate side-chains 250 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 70 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 136 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 239 optimal weight: 0.4980 chunk 133 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 302 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.049273 restraints weight = 57165.662| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.97 r_work: 0.2582 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20892 Z= 0.154 Angle : 0.615 17.510 28533 Z= 0.295 Chirality : 0.045 0.456 3426 Planarity : 0.003 0.043 3477 Dihedral : 7.429 58.655 4479 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.41 % Rotamer: Outliers : 2.06 % Allowed : 9.30 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.17), residues: 2394 helix: 2.00 (0.28), residues: 396 sheet: -0.33 (0.18), residues: 810 loop : -0.94 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 77 TYR 0.014 0.001 TYR D 484 PHE 0.012 0.001 PHE H 78 TRP 0.013 0.001 TRP F 479 HIS 0.006 0.001 HIS I 35B Details of bonding type rmsd covalent geometry : bond 0.00360 (20760) covalent geometry : angle 0.56445 (28179) SS BOND : bond 0.00206 ( 42) SS BOND : angle 0.55865 ( 84) hydrogen bonds : bond 0.03700 ( 692) hydrogen bonds : angle 4.89420 ( 1977) link_ALPHA1-3 : bond 0.01081 ( 3) link_ALPHA1-3 : angle 1.68915 ( 9) link_ALPHA1-6 : bond 0.00623 ( 3) link_ALPHA1-6 : angle 1.52337 ( 9) link_BETA1-4 : bond 0.00489 ( 24) link_BETA1-4 : angle 1.49511 ( 72) link_NAG-ASN : bond 0.00735 ( 60) link_NAG-ASN : angle 2.95861 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 0.857 Fit side-chains REVERT: E 475 MET cc_start: 0.9005 (mmm) cc_final: 0.8067 (mmm) REVERT: B 613 SER cc_start: 0.9527 (m) cc_final: 0.9259 (t) REVERT: B 621 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7770 (tm-30) REVERT: B 625 ASN cc_start: 0.9021 (t0) cc_final: 0.8717 (m-40) REVERT: B 632 ASP cc_start: 0.9129 (t70) cc_final: 0.8732 (t0) REVERT: B 657 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8406 (tm-30) REVERT: H 16 GLU cc_start: 0.8589 (pm20) cc_final: 0.8347 (pm20) REVERT: H 27 ASP cc_start: 0.9162 (t0) cc_final: 0.8961 (t0) REVERT: H 46 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7980 (mt-10) REVERT: H 72 ASP cc_start: 0.8207 (t0) cc_final: 0.7251 (t0) REVERT: H 75 LYS cc_start: 0.9107 (mtmm) cc_final: 0.8763 (mtmm) REVERT: H 100 ASP cc_start: 0.8574 (t0) cc_final: 0.8070 (t0) REVERT: L 79 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7812 (mm-30) REVERT: L 103 ARG cc_start: 0.7489 (ptm160) cc_final: 0.7098 (ptp-110) REVERT: D 166 ARG cc_start: 0.4541 (ttt-90) cc_final: 0.4262 (ttt-90) REVERT: A 621 GLU cc_start: 0.8967 (tt0) cc_final: 0.8252 (tm-30) REVERT: A 625 ASN cc_start: 0.9250 (t0) cc_final: 0.8590 (t0) REVERT: G 5 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8285 (tp-100) REVERT: G 16 GLU cc_start: 0.8338 (pm20) cc_final: 0.7775 (pm20) REVERT: G 27 ASP cc_start: 0.8904 (t0) cc_final: 0.8336 (t0) REVERT: G 100 ASP cc_start: 0.8695 (t0) cc_final: 0.8270 (t0) REVERT: J 6 GLN cc_start: 0.8426 (mt0) cc_final: 0.7924 (mt0) REVERT: J 79 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7834 (mm-30) REVERT: J 82 ASP cc_start: 0.8217 (m-30) cc_final: 0.7923 (m-30) REVERT: J 100 GLN cc_start: 0.8708 (pm20) cc_final: 0.8206 (pm20) REVERT: F 166 ARG cc_start: 0.4269 (tpt170) cc_final: 0.1217 (tmt170) REVERT: C 621 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7916 (tm-30) REVERT: C 659 ASP cc_start: 0.8734 (t0) cc_final: 0.8331 (m-30) REVERT: I 5 GLN cc_start: 0.8475 (tp-100) cc_final: 0.8125 (tp40) REVERT: I 27 ASP cc_start: 0.9282 (t70) cc_final: 0.8905 (t0) REVERT: I 72 ASP cc_start: 0.8634 (t70) cc_final: 0.8177 (t0) REVERT: I 100 TYR cc_start: 0.8399 (m-80) cc_final: 0.8026 (m-80) REVERT: I 100 ASP cc_start: 0.8345 (t70) cc_final: 0.7881 (t70) REVERT: K 24 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7774 (tmm160) outliers start: 44 outliers final: 36 residues processed: 262 average time/residue: 0.1582 time to fit residues: 62.6741 Evaluate side-chains 259 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 51 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 218 optimal weight: 20.0000 chunk 122 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 198 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.068091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.050484 restraints weight = 56684.023| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.97 r_work: 0.2642 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20892 Z= 0.112 Angle : 0.589 16.976 28533 Z= 0.282 Chirality : 0.044 0.434 3426 Planarity : 0.003 0.043 3477 Dihedral : 7.021 56.774 4479 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.66 % Rotamer: Outliers : 1.64 % Allowed : 10.33 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2394 helix: 2.07 (0.28), residues: 396 sheet: -0.24 (0.18), residues: 810 loop : -0.89 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 273 TYR 0.019 0.001 TYR D 484 PHE 0.009 0.001 PHE H 78 TRP 0.018 0.001 TRP B 571 HIS 0.006 0.001 HIS I 35B Details of bonding type rmsd covalent geometry : bond 0.00253 (20760) covalent geometry : angle 0.53792 (28179) SS BOND : bond 0.00166 ( 42) SS BOND : angle 0.46622 ( 84) hydrogen bonds : bond 0.03352 ( 692) hydrogen bonds : angle 4.70801 ( 1977) link_ALPHA1-3 : bond 0.01118 ( 3) link_ALPHA1-3 : angle 1.48680 ( 9) link_ALPHA1-6 : bond 0.00727 ( 3) link_ALPHA1-6 : angle 1.43672 ( 9) link_BETA1-4 : bond 0.00489 ( 24) link_BETA1-4 : angle 1.37454 ( 72) link_NAG-ASN : bond 0.00612 ( 60) link_NAG-ASN : angle 2.95028 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 0.836 Fit side-chains REVERT: E 475 MET cc_start: 0.9087 (mmm) cc_final: 0.8178 (mmm) REVERT: B 613 SER cc_start: 0.9478 (m) cc_final: 0.9272 (t) REVERT: B 621 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7936 (tm-30) REVERT: B 625 ASN cc_start: 0.9065 (t0) cc_final: 0.8822 (m-40) REVERT: B 632 ASP cc_start: 0.9197 (t70) cc_final: 0.8771 (t0) REVERT: B 657 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8453 (tm-30) REVERT: H 27 ASP cc_start: 0.9162 (t0) cc_final: 0.8943 (t0) REVERT: H 46 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7996 (mt-10) REVERT: H 72 ASP cc_start: 0.8328 (t0) cc_final: 0.7340 (t0) REVERT: H 75 LYS cc_start: 0.9135 (mtmm) cc_final: 0.8762 (mtmm) REVERT: H 86 ASP cc_start: 0.8717 (m-30) cc_final: 0.8486 (m-30) REVERT: H 100 ASP cc_start: 0.8565 (t0) cc_final: 0.8048 (t0) REVERT: L 79 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7809 (mm-30) REVERT: L 81 GLU cc_start: 0.8387 (pm20) cc_final: 0.8164 (pp20) REVERT: L 103 ARG cc_start: 0.7551 (ptm160) cc_final: 0.7173 (ptp-110) REVERT: D 166 ARG cc_start: 0.4673 (ttt-90) cc_final: 0.4410 (ttt-90) REVERT: D 479 TRP cc_start: 0.8620 (m-10) cc_final: 0.8364 (m-10) REVERT: A 606 THR cc_start: 0.9450 (m) cc_final: 0.9227 (p) REVERT: A 621 GLU cc_start: 0.8955 (tt0) cc_final: 0.8325 (tm-30) REVERT: A 625 ASN cc_start: 0.9216 (t0) cc_final: 0.8553 (t0) REVERT: A 632 ASP cc_start: 0.9159 (t70) cc_final: 0.8867 (t0) REVERT: G 16 GLU cc_start: 0.8363 (pm20) cc_final: 0.7948 (pm20) REVERT: G 27 ASP cc_start: 0.8933 (t0) cc_final: 0.8331 (t0) REVERT: G 100 ASP cc_start: 0.8652 (t0) cc_final: 0.8253 (t0) REVERT: J 6 GLN cc_start: 0.8397 (mt0) cc_final: 0.7979 (mt0) REVERT: J 79 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7874 (mm-30) REVERT: J 82 ASP cc_start: 0.8369 (m-30) cc_final: 0.8070 (m-30) REVERT: J 100 GLN cc_start: 0.8746 (pm20) cc_final: 0.8263 (pm20) REVERT: F 166 ARG cc_start: 0.4212 (tpt170) cc_final: 0.1715 (tpt170) REVERT: C 621 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7993 (tm-30) REVERT: C 659 ASP cc_start: 0.8765 (t0) cc_final: 0.8380 (m-30) REVERT: I 3 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7789 (mm-40) REVERT: I 5 GLN cc_start: 0.8479 (tp-100) cc_final: 0.8125 (tp40) REVERT: I 27 ASP cc_start: 0.9274 (t70) cc_final: 0.8922 (t0) REVERT: I 72 ASP cc_start: 0.8684 (t70) cc_final: 0.8219 (t0) REVERT: I 100 TYR cc_start: 0.8417 (m-80) cc_final: 0.8071 (m-80) REVERT: I 100 ASP cc_start: 0.8237 (t70) cc_final: 0.7676 (t70) outliers start: 35 outliers final: 29 residues processed: 266 average time/residue: 0.1602 time to fit residues: 64.5312 Evaluate side-chains 260 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 231 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 1 ASP Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 145 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 219 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.067489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.049901 restraints weight = 57502.144| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.91 r_work: 0.2688 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20892 Z= 0.173 Angle : 0.623 17.278 28533 Z= 0.299 Chirality : 0.045 0.428 3426 Planarity : 0.003 0.044 3477 Dihedral : 7.010 57.531 4479 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 2.06 % Allowed : 10.89 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2394 helix: 2.09 (0.28), residues: 396 sheet: -0.27 (0.18), residues: 813 loop : -0.88 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 273 TYR 0.018 0.001 TYR D 484 PHE 0.013 0.001 PHE H 78 TRP 0.015 0.001 TRP B 571 HIS 0.005 0.001 HIS I 35B Details of bonding type rmsd covalent geometry : bond 0.00411 (20760) covalent geometry : angle 0.57420 (28179) SS BOND : bond 0.00285 ( 42) SS BOND : angle 0.60038 ( 84) hydrogen bonds : bond 0.03626 ( 692) hydrogen bonds : angle 4.72950 ( 1977) link_ALPHA1-3 : bond 0.01022 ( 3) link_ALPHA1-3 : angle 1.51225 ( 9) link_ALPHA1-6 : bond 0.00534 ( 3) link_ALPHA1-6 : angle 1.51782 ( 9) link_BETA1-4 : bond 0.00478 ( 24) link_BETA1-4 : angle 1.43790 ( 72) link_NAG-ASN : bond 0.00544 ( 60) link_NAG-ASN : angle 2.94889 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 0.956 Fit side-chains REVERT: E 475 MET cc_start: 0.9160 (mmm) cc_final: 0.8403 (mmm) REVERT: B 632 ASP cc_start: 0.9323 (t70) cc_final: 0.8886 (t0) REVERT: B 657 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8516 (tm-30) REVERT: H 16 GLU cc_start: 0.8788 (pm20) cc_final: 0.8542 (pm20) REVERT: H 46 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8185 (mt-10) REVERT: H 72 ASP cc_start: 0.8488 (t0) cc_final: 0.7492 (t0) REVERT: H 75 LYS cc_start: 0.9159 (mtmm) cc_final: 0.8775 (mtmm) REVERT: H 86 ASP cc_start: 0.8871 (m-30) cc_final: 0.8472 (m-30) REVERT: H 100 ASP cc_start: 0.8630 (t0) cc_final: 0.8214 (t0) REVERT: L 79 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8008 (mm-30) REVERT: L 81 GLU cc_start: 0.8446 (pm20) cc_final: 0.8160 (pp20) REVERT: L 103 ARG cc_start: 0.7782 (ptm160) cc_final: 0.7395 (ptp-110) REVERT: D 166 ARG cc_start: 0.4813 (ttt-90) cc_final: 0.4438 (ttt-90) REVERT: A 621 GLU cc_start: 0.9009 (tt0) cc_final: 0.8464 (tm-30) REVERT: A 625 ASN cc_start: 0.9230 (t0) cc_final: 0.8560 (t0) REVERT: G 16 GLU cc_start: 0.8408 (pm20) cc_final: 0.8009 (pm20) REVERT: G 27 ASP cc_start: 0.9046 (t0) cc_final: 0.8470 (t0) REVERT: G 100 ASP cc_start: 0.8696 (t0) cc_final: 0.8331 (t0) REVERT: J 6 GLN cc_start: 0.8637 (mt0) cc_final: 0.8181 (mt0) REVERT: J 79 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8076 (mm-30) REVERT: J 100 GLN cc_start: 0.8780 (pm20) cc_final: 0.8313 (pm20) REVERT: F 166 ARG cc_start: 0.4524 (tpt170) cc_final: 0.1568 (tmt170) REVERT: C 621 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8150 (tm-30) REVERT: C 657 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8683 (tm-30) REVERT: C 659 ASP cc_start: 0.8895 (t0) cc_final: 0.8526 (m-30) REVERT: I 5 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8206 (tp40) REVERT: I 27 ASP cc_start: 0.9224 (t70) cc_final: 0.8913 (t0) REVERT: I 72 ASP cc_start: 0.8785 (t70) cc_final: 0.8341 (t0) REVERT: I 100 ASP cc_start: 0.8385 (t70) cc_final: 0.7922 (t70) outliers start: 44 outliers final: 39 residues processed: 263 average time/residue: 0.1552 time to fit residues: 62.5658 Evaluate side-chains 265 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 190 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 88 optimal weight: 0.0870 chunk 43 optimal weight: 2.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.072185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.053757 restraints weight = 59428.452| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.95 r_work: 0.2720 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20892 Z= 0.110 Angle : 0.592 17.987 28533 Z= 0.283 Chirality : 0.044 0.412 3426 Planarity : 0.003 0.044 3477 Dihedral : 6.755 56.351 4479 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 1.64 % Allowed : 11.73 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2394 helix: 2.09 (0.28), residues: 399 sheet: -0.11 (0.18), residues: 789 loop : -0.82 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 273 TYR 0.022 0.001 TYR D 484 PHE 0.009 0.001 PHE D 53 TRP 0.021 0.001 TRP B 571 HIS 0.005 0.001 HIS I 35B Details of bonding type rmsd covalent geometry : bond 0.00249 (20760) covalent geometry : angle 0.54330 (28179) SS BOND : bond 0.00167 ( 42) SS BOND : angle 0.46695 ( 84) hydrogen bonds : bond 0.03206 ( 692) hydrogen bonds : angle 4.58800 ( 1977) link_ALPHA1-3 : bond 0.01071 ( 3) link_ALPHA1-3 : angle 1.26213 ( 9) link_ALPHA1-6 : bond 0.00601 ( 3) link_ALPHA1-6 : angle 1.42569 ( 9) link_BETA1-4 : bond 0.00496 ( 24) link_BETA1-4 : angle 1.28873 ( 72) link_NAG-ASN : bond 0.00530 ( 60) link_NAG-ASN : angle 2.89658 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 1.015 Fit side-chains REVERT: E 475 MET cc_start: 0.9158 (mmm) cc_final: 0.8362 (mmm) REVERT: B 632 ASP cc_start: 0.9285 (t70) cc_final: 0.8837 (t0) REVERT: B 657 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8498 (tm-30) REVERT: H 46 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8112 (mt-10) REVERT: H 72 ASP cc_start: 0.8447 (t0) cc_final: 0.7419 (t0) REVERT: H 75 LYS cc_start: 0.9159 (mtmm) cc_final: 0.8767 (mtmm) REVERT: H 86 ASP cc_start: 0.8792 (m-30) cc_final: 0.8400 (m-30) REVERT: H 100 ASP cc_start: 0.8613 (t0) cc_final: 0.8137 (t0) REVERT: L 79 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7925 (mm-30) REVERT: L 81 GLU cc_start: 0.8459 (pm20) cc_final: 0.8144 (pp20) REVERT: L 103 ARG cc_start: 0.7709 (ptm160) cc_final: 0.7346 (ptp-110) REVERT: D 166 ARG cc_start: 0.4726 (ttt-90) cc_final: 0.4373 (ttt-90) REVERT: D 207 LYS cc_start: 0.7798 (tptp) cc_final: 0.7512 (tmtt) REVERT: A 621 GLU cc_start: 0.8961 (tt0) cc_final: 0.8415 (tm-30) REVERT: A 625 ASN cc_start: 0.9196 (t0) cc_final: 0.8507 (t0) REVERT: A 632 ASP cc_start: 0.9235 (t70) cc_final: 0.8933 (t0) REVERT: G 16 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7982 (pm20) REVERT: G 27 ASP cc_start: 0.9016 (t0) cc_final: 0.8420 (t0) REVERT: G 100 ASP cc_start: 0.8608 (t0) cc_final: 0.8261 (t0) REVERT: J 6 GLN cc_start: 0.8452 (mt0) cc_final: 0.8109 (mt0) REVERT: J 79 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8035 (mm-30) REVERT: J 100 GLN cc_start: 0.8755 (pm20) cc_final: 0.8294 (pm20) REVERT: F 166 ARG cc_start: 0.4442 (tpt170) cc_final: 0.2642 (tpt90) REVERT: C 621 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8127 (tm-30) REVERT: C 659 ASP cc_start: 0.8869 (t0) cc_final: 0.8498 (m-30) REVERT: I 5 GLN cc_start: 0.8561 (tp-100) cc_final: 0.8213 (tp40) REVERT: I 27 ASP cc_start: 0.9226 (t70) cc_final: 0.8885 (t0) REVERT: I 72 ASP cc_start: 0.8772 (t70) cc_final: 0.8322 (t0) REVERT: I 100 ILE cc_start: 0.9316 (mm) cc_final: 0.8984 (mm) REVERT: I 100 ASP cc_start: 0.8245 (t70) cc_final: 0.7726 (t70) outliers start: 35 outliers final: 33 residues processed: 268 average time/residue: 0.1602 time to fit residues: 65.6824 Evaluate side-chains 264 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 40 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 228 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 180 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.071767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.053227 restraints weight = 59263.461| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.94 r_work: 0.2698 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20892 Z= 0.140 Angle : 0.607 17.505 28533 Z= 0.291 Chirality : 0.044 0.403 3426 Planarity : 0.003 0.041 3477 Dihedral : 6.761 56.844 4479 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.59 % Favored : 96.37 % Rotamer: Outliers : 1.96 % Allowed : 11.97 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.17), residues: 2394 helix: 2.08 (0.28), residues: 399 sheet: -0.09 (0.18), residues: 789 loop : -0.82 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 273 TYR 0.023 0.001 TYR D 484 PHE 0.011 0.001 PHE H 78 TRP 0.016 0.001 TRP B 571 HIS 0.004 0.001 HIS I 35B Details of bonding type rmsd covalent geometry : bond 0.00331 (20760) covalent geometry : angle 0.56107 (28179) SS BOND : bond 0.00189 ( 42) SS BOND : angle 0.53137 ( 84) hydrogen bonds : bond 0.03335 ( 692) hydrogen bonds : angle 4.57407 ( 1977) link_ALPHA1-3 : bond 0.00947 ( 3) link_ALPHA1-3 : angle 1.30017 ( 9) link_ALPHA1-6 : bond 0.00470 ( 3) link_ALPHA1-6 : angle 1.50045 ( 9) link_BETA1-4 : bond 0.00492 ( 24) link_BETA1-4 : angle 1.34561 ( 72) link_NAG-ASN : bond 0.00518 ( 60) link_NAG-ASN : angle 2.85767 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 0.944 Fit side-chains REVERT: E 475 MET cc_start: 0.9167 (mmm) cc_final: 0.8383 (mmm) REVERT: B 632 ASP cc_start: 0.9306 (t70) cc_final: 0.8856 (t0) REVERT: B 657 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8495 (tm-30) REVERT: H 46 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8111 (mt-10) REVERT: H 72 ASP cc_start: 0.8458 (t0) cc_final: 0.7422 (t0) REVERT: H 75 LYS cc_start: 0.9156 (mtmm) cc_final: 0.8754 (mtmm) REVERT: H 100 ASP cc_start: 0.8647 (t0) cc_final: 0.8243 (t0) REVERT: L 79 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7994 (mm-30) REVERT: L 81 GLU cc_start: 0.8496 (pm20) cc_final: 0.8179 (pp20) REVERT: L 103 ARG cc_start: 0.7727 (ptm160) cc_final: 0.7365 (ptp-110) REVERT: D 166 ARG cc_start: 0.4709 (ttt-90) cc_final: 0.4345 (ttt-90) REVERT: D 207 LYS cc_start: 0.7819 (tptp) cc_final: 0.7515 (tmtt) REVERT: A 621 GLU cc_start: 0.8996 (tt0) cc_final: 0.8475 (tm-30) REVERT: A 625 ASN cc_start: 0.9205 (t0) cc_final: 0.8507 (t0) REVERT: A 632 ASP cc_start: 0.9255 (t70) cc_final: 0.8954 (t0) REVERT: G 16 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7982 (pm20) REVERT: G 27 ASP cc_start: 0.9015 (t0) cc_final: 0.8416 (t0) REVERT: G 100 ASP cc_start: 0.8654 (t0) cc_final: 0.8312 (t0) REVERT: G 105 GLN cc_start: 0.9081 (pt0) cc_final: 0.8630 (pm20) REVERT: J 6 GLN cc_start: 0.8555 (mt0) cc_final: 0.8149 (mt0) REVERT: J 79 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8082 (mm-30) REVERT: J 100 GLN cc_start: 0.8741 (pm20) cc_final: 0.8274 (pm20) REVERT: F 166 ARG cc_start: 0.4564 (tpt170) cc_final: 0.1254 (ttt-90) REVERT: C 621 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8141 (tm-30) REVERT: C 659 ASP cc_start: 0.8889 (t0) cc_final: 0.8525 (m-30) REVERT: I 5 GLN cc_start: 0.8564 (tp-100) cc_final: 0.8209 (tp40) REVERT: I 27 ASP cc_start: 0.9220 (t70) cc_final: 0.8872 (t0) REVERT: I 72 ASP cc_start: 0.8777 (t70) cc_final: 0.8328 (t0) REVERT: I 100 ILE cc_start: 0.9333 (mm) cc_final: 0.9020 (mm) REVERT: I 100 ASP cc_start: 0.8323 (t70) cc_final: 0.7856 (t70) outliers start: 42 outliers final: 38 residues processed: 265 average time/residue: 0.1560 time to fit residues: 63.1679 Evaluate side-chains 270 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 100 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 167 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 172 optimal weight: 0.4980 chunk 174 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.067526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.049966 restraints weight = 57636.294| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.93 r_work: 0.2686 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20892 Z= 0.173 Angle : 0.629 17.268 28533 Z= 0.302 Chirality : 0.045 0.398 3426 Planarity : 0.003 0.039 3477 Dihedral : 6.827 58.875 4479 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 1.92 % Allowed : 12.01 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2394 helix: 2.07 (0.28), residues: 399 sheet: -0.09 (0.18), residues: 789 loop : -0.83 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 273 TYR 0.023 0.001 TYR D 484 PHE 0.012 0.001 PHE H 78 TRP 0.017 0.001 TRP B 571 HIS 0.005 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00411 (20760) covalent geometry : angle 0.58401 (28179) SS BOND : bond 0.00220 ( 42) SS BOND : angle 0.58962 ( 84) hydrogen bonds : bond 0.03487 ( 692) hydrogen bonds : angle 4.61495 ( 1977) link_ALPHA1-3 : bond 0.00923 ( 3) link_ALPHA1-3 : angle 1.27715 ( 9) link_ALPHA1-6 : bond 0.00410 ( 3) link_ALPHA1-6 : angle 1.52999 ( 9) link_BETA1-4 : bond 0.00485 ( 24) link_BETA1-4 : angle 1.34975 ( 72) link_NAG-ASN : bond 0.00520 ( 60) link_NAG-ASN : angle 2.87419 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 0.853 Fit side-chains REVERT: E 475 MET cc_start: 0.9151 (mmm) cc_final: 0.8375 (mmm) REVERT: B 632 ASP cc_start: 0.9316 (t70) cc_final: 0.8859 (t0) REVERT: B 657 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8497 (tm-30) REVERT: H 46 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8136 (mt-10) REVERT: H 72 ASP cc_start: 0.8472 (t0) cc_final: 0.7535 (t0) REVERT: H 75 LYS cc_start: 0.9166 (mtmm) cc_final: 0.8864 (mtmm) REVERT: H 100 ASP cc_start: 0.8682 (t0) cc_final: 0.8232 (t0) REVERT: L 79 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8011 (mm-30) REVERT: L 81 GLU cc_start: 0.8488 (pm20) cc_final: 0.8184 (pp20) REVERT: L 103 ARG cc_start: 0.7743 (ptm160) cc_final: 0.7370 (ptp-110) REVERT: D 166 ARG cc_start: 0.4749 (ttt-90) cc_final: 0.4378 (ttt-90) REVERT: D 207 LYS cc_start: 0.7856 (tptp) cc_final: 0.7545 (tmtt) REVERT: A 621 GLU cc_start: 0.8971 (tt0) cc_final: 0.8462 (tm-30) REVERT: A 625 ASN cc_start: 0.9185 (t0) cc_final: 0.8462 (t0) REVERT: G 16 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7988 (pm20) REVERT: G 27 ASP cc_start: 0.9049 (t0) cc_final: 0.8457 (t0) REVERT: G 100 ASP cc_start: 0.8678 (t0) cc_final: 0.8355 (t0) REVERT: G 105 GLN cc_start: 0.9080 (pt0) cc_final: 0.8631 (pm20) REVERT: J 6 GLN cc_start: 0.8597 (mt0) cc_final: 0.8167 (mt0) REVERT: J 79 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8092 (mm-30) REVERT: J 100 GLN cc_start: 0.8745 (pm20) cc_final: 0.8282 (pm20) REVERT: F 166 ARG cc_start: 0.4514 (tpt170) cc_final: 0.1066 (ttt90) REVERT: C 621 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8139 (tm-30) REVERT: C 659 ASP cc_start: 0.8895 (t0) cc_final: 0.8535 (m-30) REVERT: I 27 ASP cc_start: 0.9217 (t70) cc_final: 0.8866 (t0) REVERT: I 72 ASP cc_start: 0.8791 (t70) cc_final: 0.8348 (t0) REVERT: I 100 ILE cc_start: 0.9358 (mm) cc_final: 0.9048 (mm) REVERT: I 100 ASP cc_start: 0.8385 (t70) cc_final: 0.7920 (t70) outliers start: 41 outliers final: 37 residues processed: 261 average time/residue: 0.1613 time to fit residues: 64.1037 Evaluate side-chains 263 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 225 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 217 optimal weight: 0.4980 chunk 124 optimal weight: 0.7980 chunk 165 optimal weight: 0.0970 chunk 93 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 202 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN A 652 GLN I 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.072538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.054187 restraints weight = 59064.984| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.94 r_work: 0.2727 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20892 Z= 0.100 Angle : 0.595 17.941 28533 Z= 0.285 Chirality : 0.043 0.388 3426 Planarity : 0.003 0.039 3477 Dihedral : 6.593 56.055 4479 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.57 % Rotamer: Outliers : 1.87 % Allowed : 12.20 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2394 helix: 2.09 (0.28), residues: 399 sheet: -0.06 (0.18), residues: 807 loop : -0.83 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 273 TYR 0.022 0.001 TYR D 484 PHE 0.008 0.001 PHE H 78 TRP 0.015 0.001 TRP E 96 HIS 0.005 0.001 HIS I 35B Details of bonding type rmsd covalent geometry : bond 0.00226 (20760) covalent geometry : angle 0.55002 (28179) SS BOND : bond 0.00149 ( 42) SS BOND : angle 0.45226 ( 84) hydrogen bonds : bond 0.03060 ( 692) hydrogen bonds : angle 4.48895 ( 1977) link_ALPHA1-3 : bond 0.00962 ( 3) link_ALPHA1-3 : angle 1.17974 ( 9) link_ALPHA1-6 : bond 0.00518 ( 3) link_ALPHA1-6 : angle 1.44720 ( 9) link_BETA1-4 : bond 0.00504 ( 24) link_BETA1-4 : angle 1.24538 ( 72) link_NAG-ASN : bond 0.00518 ( 60) link_NAG-ASN : angle 2.80903 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6249.92 seconds wall clock time: 107 minutes 53.78 seconds (6473.78 seconds total)