Starting phenix.real_space_refine on Tue May 20 21:46:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8to7_41438/05_2025/8to7_41438.cif Found real_map, /net/cci-nas-00/data/ceres_data/8to7_41438/05_2025/8to7_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_41438/05_2025/8to7_41438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8to7_41438/05_2025/8to7_41438.map" model { file = "/net/cci-nas-00/data/ceres_data/8to7_41438/05_2025/8to7_41438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8to7_41438/05_2025/8to7_41438.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 22.95, per 1000 atoms: 1.13 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: 5.11 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.71 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: 7.43 Time building geometry restraints manager: 6.01 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: 47.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 58.820 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.049 0.002 TRP D 427 HIS 0.025 0.002 HIS I 35B PHE 0.018 0.002 PHE E 233 TYR 0.034 0.002 TYR D 486 ARG 0.011 0.001 ARG D 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 60) link_NAG-ASN : angle 3.13279 ( 180) 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_ALPHA1-3 : bond 0.00570 ( 3) link_ALPHA1-3 : angle 1.20891 ( 9) hydrogen bonds : bond 0.23818 ( 692) hydrogen bonds : angle 8.29025 ( 1977) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.30042 ( 84) covalent geometry : bond 0.00628 (20760) covalent geometry : angle 1.09252 (28179) *********************** 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 : 2.178 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 293 GLN cc_start: 0.8535 (mt0) cc_final: 0.8335 (mt0) 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: 0.8948 (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: 0.7757 (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: 0.3546 time to fit residues: 161.9521 Evaluate side-chains 237 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 F 352 HIS 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 = 0.3181 r_free = 0.3181 target = 0.069300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.050797 restraints weight = 58510.948| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 4.15 r_work: 0.2606 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 20892 Z= 0.269 Angle : 0.738 12.207 28533 Z= 0.363 Chirality : 0.050 0.501 3426 Planarity : 0.004 0.055 3477 Dihedral : 10.848 77.569 4479 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.45 % Allowed : 6.31 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2394 helix: 1.56 (0.28), residues: 408 sheet: -0.58 (0.18), residues: 753 loop : -0.96 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 571 HIS 0.008 0.001 HIS F 105 PHE 0.017 0.002 PHE D 383 TYR 0.016 0.002 TYR B 638 ARG 0.006 0.001 ARG C 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 60) link_NAG-ASN : angle 2.74241 ( 180) link_ALPHA1-6 : bond 0.00134 ( 3) link_ALPHA1-6 : angle 2.05380 ( 9) link_BETA1-4 : bond 0.00717 ( 24) link_BETA1-4 : angle 2.29856 ( 72) link_ALPHA1-3 : bond 0.00829 ( 3) link_ALPHA1-3 : angle 2.84956 ( 9) hydrogen bonds : bond 0.04673 ( 692) hydrogen bonds : angle 5.85737 ( 1977) SS BOND : bond 0.00356 ( 42) SS BOND : angle 0.97894 ( 84) covalent geometry : bond 0.00638 (20760) covalent geometry : angle 0.69494 (28179) *********************** 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 276 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 245 time to evaluate : 2.136 Fit side-chains REVERT: E 161 MET cc_start: 0.8815 (tpt) cc_final: 0.8444 (tpt) REVERT: E 377 ASN cc_start: 0.9242 (p0) cc_final: 0.9040 (p0) REVERT: E 475 MET cc_start: 0.9016 (mmm) cc_final: 0.8696 (tpp) REVERT: B 621 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7981 (tm-30) REVERT: B 625 ASN cc_start: 0.9055 (t0) cc_final: 0.8577 (t0) REVERT: B 632 ASP cc_start: 0.9175 (t0) cc_final: 0.8836 (t0) REVERT: H 16 GLU cc_start: 0.8665 (pm20) cc_final: 0.8422 (pm20) REVERT: H 46 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8337 (mt-10) REVERT: H 72 ASP cc_start: 0.8049 (t70) cc_final: 0.7398 (t0) REVERT: H 75 LYS cc_start: 0.8994 (mtmm) cc_final: 0.8707 (mtmm) REVERT: H 100 TYR cc_start: 0.8743 (m-80) cc_final: 0.8358 (m-80) REVERT: H 100 ASP cc_start: 0.8509 (t0) cc_final: 0.8246 (t0) REVERT: L 79 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7494 (mm-30) REVERT: L 103 ARG cc_start: 0.7631 (ptm160) cc_final: 0.7145 (ptp-110) REVERT: D 166 ARG cc_start: 0.4860 (ttt-90) cc_final: 0.4428 (ttt-90) REVERT: A 621 GLU cc_start: 0.8990 (tt0) cc_final: 0.8160 (tm-30) REVERT: A 625 ASN cc_start: 0.9236 (t0) cc_final: 0.8645 (t0) REVERT: G 3 GLN cc_start: 0.8503 (mm110) cc_final: 0.8284 (mm110) REVERT: G 5 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8320 (tp-100) REVERT: G 16 GLU cc_start: 0.8243 (pm20) cc_final: 0.7659 (pm20) REVERT: G 72 ASP cc_start: 0.8079 (p0) cc_final: 0.7637 (p0) REVERT: G 75 LYS cc_start: 0.8518 (ptpp) cc_final: 0.8318 (pttm) REVERT: G 100 ASP cc_start: 0.8709 (t0) cc_final: 0.8343 (t0) REVERT: G 105 GLN cc_start: 0.8975 (pt0) cc_final: 0.8642 (pt0) REVERT: G 111 VAL cc_start: 0.9333 (t) cc_final: 0.9041 (m) REVERT: J 17 GLU cc_start: 0.7188 (pm20) cc_final: 0.6967 (pm20) REVERT: J 79 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7671 (mm-30) REVERT: J 82 ASP cc_start: 0.8148 (m-30) cc_final: 0.7647 (m-30) REVERT: F 166 ARG cc_start: 0.4596 (tpt170) cc_final: 0.1252 (tmt170) REVERT: F 475 MET cc_start: 0.8876 (tpp) cc_final: 0.8647 (tpp) REVERT: C 621 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7964 (tm-30) REVERT: I 5 GLN cc_start: 0.8544 (tp-100) cc_final: 0.8103 (tp40) REVERT: I 27 ASP cc_start: 0.9271 (t70) cc_final: 0.8859 (t70) REVERT: I 72 ASP cc_start: 0.8740 (t70) cc_final: 0.8434 (t0) REVERT: I 100 ILE cc_start: 0.9037 (mm) cc_final: 0.8623 (mm) REVERT: I 100 ASP cc_start: 0.8479 (t0) cc_final: 0.8227 (t70) REVERT: K 24 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7638 (tmm160) REVERT: K 81 GLU cc_start: 0.8224 (pm20) cc_final: 0.8016 (pm20) outliers start: 31 outliers final: 25 residues processed: 262 average time/residue: 0.3400 time to fit residues: 134.5359 Evaluate side-chains 244 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 2.107 ------------------------------------------------------------------------------- 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 B residue 660 LEU Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 97 THR 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 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 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 83 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 28 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 GLN ** 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 = 0.3140 r_free = 0.3140 target = 0.067352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.049276 restraints weight = 56973.834| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.90 r_work: 0.2575 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2495 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= 0.216 Angle : 0.674 11.985 28533 Z= 0.326 Chirality : 0.048 0.488 3426 Planarity : 0.004 0.049 3477 Dihedral : 8.866 67.040 4479 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.66 % Rotamer: Outliers : 1.68 % Allowed : 8.23 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2394 helix: 1.63 (0.28), residues: 405 sheet: -0.65 (0.17), residues: 825 loop : -0.94 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 479 HIS 0.010 0.001 HIS I 35B PHE 0.015 0.002 PHE D 53 TYR 0.013 0.001 TYR D 484 ARG 0.006 0.001 ARG C 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 60) link_NAG-ASN : angle 2.85373 ( 180) link_ALPHA1-6 : bond 0.00490 ( 3) link_ALPHA1-6 : angle 1.83642 ( 9) link_BETA1-4 : bond 0.00586 ( 24) link_BETA1-4 : angle 1.92788 ( 72) link_ALPHA1-3 : bond 0.01007 ( 3) link_ALPHA1-3 : angle 1.69183 ( 9) hydrogen bonds : bond 0.04432 ( 692) hydrogen bonds : angle 5.37151 ( 1977) SS BOND : bond 0.00280 ( 42) SS BOND : angle 0.71173 ( 84) covalent geometry : bond 0.00507 (20760) covalent geometry : angle 0.62829 (28179) *********************** 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 272 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 2.130 Fit side-chains REVERT: E 475 MET cc_start: 0.8874 (mmm) cc_final: 0.8445 (tpp) REVERT: B 621 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7912 (tm-30) REVERT: B 625 ASN cc_start: 0.9012 (t0) cc_final: 0.8533 (t0) REVERT: B 632 ASP cc_start: 0.9152 (t70) cc_final: 0.8766 (t0) REVERT: H 27 ASP cc_start: 0.9260 (t0) cc_final: 0.9057 (t0) REVERT: H 46 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8099 (mt-10) REVERT: H 72 ASP cc_start: 0.7899 (t70) cc_final: 0.7153 (t0) REVERT: H 75 LYS cc_start: 0.9014 (mtmm) cc_final: 0.8532 (mtmm) REVERT: H 100 TYR cc_start: 0.8856 (m-80) cc_final: 0.8412 (m-80) REVERT: H 100 ASP cc_start: 0.8583 (t0) cc_final: 0.8120 (t0) REVERT: L 79 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7689 (mm-30) REVERT: L 103 ARG cc_start: 0.7562 (ptm160) cc_final: 0.7101 (ptp-110) REVERT: D 166 ARG cc_start: 0.4636 (ttt-90) cc_final: 0.4436 (ttt-90) REVERT: A 621 GLU cc_start: 0.8987 (tt0) cc_final: 0.8153 (tm-30) REVERT: A 625 ASN cc_start: 0.9260 (t0) cc_final: 0.8538 (t0) REVERT: G 3 GLN cc_start: 0.8438 (mm110) cc_final: 0.8216 (mm110) REVERT: G 5 GLN cc_start: 0.8580 (tp-100) cc_final: 0.8349 (tp-100) REVERT: G 16 GLU cc_start: 0.8318 (pm20) cc_final: 0.7663 (pm20) REVERT: G 72 ASP cc_start: 0.8042 (p0) cc_final: 0.7676 (p0) REVERT: G 75 LYS cc_start: 0.8529 (ptpp) cc_final: 0.8312 (pttm) REVERT: G 100 ASP cc_start: 0.8682 (t0) cc_final: 0.8302 (t0) REVERT: G 105 GLN cc_start: 0.9072 (pt0) cc_final: 0.8749 (pt0) REVERT: J 17 GLU cc_start: 0.7375 (pm20) cc_final: 0.7107 (pm20) REVERT: J 79 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7717 (mm-30) REVERT: J 82 ASP cc_start: 0.8166 (m-30) cc_final: 0.7799 (m-30) REVERT: F 166 ARG cc_start: 0.4512 (tpt170) cc_final: 0.1177 (tmt170) REVERT: C 621 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7868 (tm-30) REVERT: C 657 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8562 (tm-30) REVERT: C 659 ASP cc_start: 0.8695 (t0) cc_final: 0.8271 (m-30) REVERT: I 5 GLN cc_start: 0.8481 (tp-100) cc_final: 0.8095 (tp40) REVERT: I 16 GLU cc_start: 0.8339 (pm20) cc_final: 0.8012 (pm20) REVERT: I 27 ASP cc_start: 0.9284 (t70) cc_final: 0.8957 (t0) REVERT: I 72 ASP cc_start: 0.8643 (t70) cc_final: 0.8249 (t0) REVERT: I 100 ILE cc_start: 0.9142 (mm) cc_final: 0.8868 (mm) REVERT: I 100 TYR cc_start: 0.8760 (m-80) cc_final: 0.8502 (m-10) REVERT: K 24 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7757 (tmm160) outliers start: 36 outliers final: 29 residues processed: 260 average time/residue: 0.3515 time to fit residues: 137.6673 Evaluate side-chains 250 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 2.134 ------------------------------------------------------------------------------- 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 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 H residue 51 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain D residue 265 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 38 VAL 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 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 Chi-restraints excluded: chain K residue 83 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 208 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 90 optimal weight: 0.0980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN ** 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 = 0.3127 r_free = 0.3127 target = 0.066728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.048562 restraints weight = 57580.130| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.92 r_work: 0.2555 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20892 Z= 0.205 Angle : 0.663 16.394 28533 Z= 0.320 Chirality : 0.047 0.477 3426 Planarity : 0.004 0.045 3477 Dihedral : 7.854 59.661 4479 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 2.66 % Allowed : 8.84 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.17), residues: 2394 helix: 1.68 (0.28), residues: 405 sheet: -0.55 (0.18), residues: 816 loop : -1.00 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 571 HIS 0.007 0.001 HIS I 35B PHE 0.014 0.002 PHE D 53 TYR 0.014 0.001 TYR D 484 ARG 0.005 0.000 ARG J 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 60) link_NAG-ASN : angle 3.02119 ( 180) link_ALPHA1-6 : bond 0.00813 ( 3) link_ALPHA1-6 : angle 2.11522 ( 9) link_BETA1-4 : bond 0.00458 ( 24) link_BETA1-4 : angle 1.72826 ( 72) link_ALPHA1-3 : bond 0.01007 ( 3) link_ALPHA1-3 : angle 2.03523 ( 9) hydrogen bonds : bond 0.04046 ( 692) hydrogen bonds : angle 5.09630 ( 1977) SS BOND : bond 0.00256 ( 42) SS BOND : angle 0.69313 ( 84) covalent geometry : bond 0.00484 (20760) covalent geometry : angle 0.61209 (28179) *********************** 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 283 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 226 time to evaluate : 2.184 Fit side-chains REVERT: E 475 MET cc_start: 0.8802 (mmm) cc_final: 0.8321 (tpp) REVERT: B 621 GLU cc_start: 0.8234 (tm-30) cc_final: 0.8028 (tm-30) REVERT: B 625 ASN cc_start: 0.8987 (t0) cc_final: 0.8687 (m-40) REVERT: B 632 ASP cc_start: 0.9163 (t70) cc_final: 0.8754 (t0) REVERT: H 46 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8043 (mt-10) REVERT: H 72 ASP cc_start: 0.7882 (t70) cc_final: 0.7042 (t0) REVERT: H 75 LYS cc_start: 0.9005 (mtmm) cc_final: 0.8622 (mtmm) REVERT: H 100 ASP cc_start: 0.8658 (t0) cc_final: 0.8190 (t0) REVERT: L 103 ARG cc_start: 0.7502 (ptm160) cc_final: 0.7055 (ptp-110) REVERT: A 621 GLU cc_start: 0.8984 (tt0) cc_final: 0.8178 (tm-30) REVERT: A 625 ASN cc_start: 0.9320 (t0) cc_final: 0.8689 (t0) REVERT: A 632 ASP cc_start: 0.9141 (t70) cc_final: 0.8869 (t0) REVERT: G 5 GLN cc_start: 0.8575 (tp-100) cc_final: 0.8366 (tp-100) REVERT: G 16 GLU cc_start: 0.8335 (pm20) cc_final: 0.7704 (pm20) REVERT: G 27 ASP cc_start: 0.8970 (t0) cc_final: 0.8484 (t0) REVERT: G 72 ASP cc_start: 0.8078 (p0) cc_final: 0.7675 (p0) REVERT: G 75 LYS cc_start: 0.8574 (ptpp) cc_final: 0.8312 (pttm) REVERT: G 100 ASP cc_start: 0.8719 (t0) cc_final: 0.8381 (t0) REVERT: G 105 GLN cc_start: 0.9071 (pt0) cc_final: 0.8754 (pt0) REVERT: J 79 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7834 (mm-30) REVERT: F 166 ARG cc_start: 0.4280 (tpt170) cc_final: 0.0886 (tmt170) REVERT: C 621 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7893 (tm-30) REVERT: C 657 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8532 (tm-30) REVERT: I 3 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7722 (mm-40) REVERT: I 5 GLN cc_start: 0.8471 (tp-100) cc_final: 0.8096 (tp40) REVERT: I 27 ASP cc_start: 0.9270 (t70) cc_final: 0.8927 (t0) REVERT: I 72 ASP cc_start: 0.8651 (t70) cc_final: 0.8234 (t0) REVERT: I 100 ILE cc_start: 0.9190 (mm) cc_final: 0.8981 (mm) REVERT: I 100 ASP cc_start: 0.8496 (t70) cc_final: 0.8032 (t70) REVERT: K 24 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7758 (tmm160) outliers start: 57 outliers final: 40 residues processed: 265 average time/residue: 0.3415 time to fit residues: 136.8278 Evaluate side-chains 256 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 2.299 ------------------------------------------------------------------------------- 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 89 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 120 VAL 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 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 68 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 11 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 62 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 232 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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** ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.065808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.048105 restraints weight = 57956.948| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 4.02 r_work: 0.2596 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20892 Z= 0.198 Angle : 0.650 15.498 28533 Z= 0.313 Chirality : 0.046 0.459 3426 Planarity : 0.003 0.043 3477 Dihedral : 7.667 59.797 4479 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 2.62 % Allowed : 9.72 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2394 helix: 1.74 (0.28), residues: 405 sheet: -0.49 (0.18), residues: 819 loop : -1.01 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 571 HIS 0.007 0.001 HIS I 35B PHE 0.013 0.001 PHE D 53 TYR 0.019 0.001 TYR D 484 ARG 0.007 0.000 ARG F 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 60) link_NAG-ASN : angle 3.04529 ( 180) link_ALPHA1-6 : bond 0.00561 ( 3) link_ALPHA1-6 : angle 1.56405 ( 9) link_BETA1-4 : bond 0.00503 ( 24) link_BETA1-4 : angle 1.52560 ( 72) link_ALPHA1-3 : bond 0.01087 ( 3) link_ALPHA1-3 : angle 1.73860 ( 9) hydrogen bonds : bond 0.03977 ( 692) hydrogen bonds : angle 4.98051 ( 1977) SS BOND : bond 0.00247 ( 42) SS BOND : angle 0.65144 ( 84) covalent geometry : bond 0.00470 (20760) covalent geometry : angle 0.59990 (28179) *********************** 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 283 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 227 time to evaluate : 2.114 Fit side-chains revert: symmetry clash REVERT: E 475 MET cc_start: 0.9052 (mmm) cc_final: 0.7949 (mmm) REVERT: E 476 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8172 (mtt-85) REVERT: B 625 ASN cc_start: 0.9071 (t0) cc_final: 0.8835 (m-40) REVERT: B 632 ASP cc_start: 0.9293 (t70) cc_final: 0.8877 (t0) REVERT: H 46 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8211 (mt-10) REVERT: H 72 ASP cc_start: 0.8090 (t70) cc_final: 0.7261 (t0) REVERT: H 75 LYS cc_start: 0.9093 (mtmm) cc_final: 0.8683 (mtmm) REVERT: H 100 ASP cc_start: 0.8707 (t0) cc_final: 0.8275 (t0) REVERT: L 81 GLU cc_start: 0.8446 (pm20) cc_final: 0.8209 (pp20) REVERT: L 103 ARG cc_start: 0.7740 (ptm160) cc_final: 0.7325 (ptp-110) REVERT: A 621 GLU cc_start: 0.9036 (tt0) cc_final: 0.8325 (tm-30) REVERT: A 625 ASN cc_start: 0.9318 (t0) cc_final: 0.8589 (t0) REVERT: G 5 GLN cc_start: 0.8635 (tp-100) cc_final: 0.8431 (tp-100) REVERT: G 16 GLU cc_start: 0.8347 (pm20) cc_final: 0.7780 (pm20) REVERT: G 27 ASP cc_start: 0.9057 (t0) cc_final: 0.8524 (t0) REVERT: G 72 ASP cc_start: 0.8090 (p0) cc_final: 0.7674 (p0) REVERT: G 75 LYS cc_start: 0.8620 (ptpp) cc_final: 0.8329 (pttm) REVERT: G 100 ASP cc_start: 0.8674 (t0) cc_final: 0.8398 (t0) REVERT: G 105 GLN cc_start: 0.9047 (pt0) cc_final: 0.8722 (pt0) REVERT: J 6 GLN cc_start: 0.8604 (mt0) cc_final: 0.8300 (mt0) REVERT: J 79 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8019 (mm-30) REVERT: J 100 GLN cc_start: 0.8845 (pm20) cc_final: 0.8486 (pm20) REVERT: F 166 ARG cc_start: 0.4481 (tpt170) cc_final: 0.1256 (tmt170) REVERT: C 621 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8014 (tm-30) REVERT: C 657 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8651 (tm-30) REVERT: C 659 ASP cc_start: 0.8763 (t0) cc_final: 0.8391 (m-30) REVERT: I 3 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7795 (mm-40) REVERT: I 5 GLN cc_start: 0.8527 (tp-100) cc_final: 0.8172 (tp40) REVERT: I 27 ASP cc_start: 0.9242 (t70) cc_final: 0.8920 (t0) REVERT: I 72 ASP cc_start: 0.8744 (t70) cc_final: 0.8322 (t0) REVERT: I 100 ASP cc_start: 0.8487 (t70) cc_final: 0.7970 (t70) REVERT: K 24 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7875 (tmm160) outliers start: 56 outliers final: 49 residues processed: 269 average time/residue: 0.3459 time to fit residues: 140.2781 Evaluate side-chains 268 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 217 time to evaluate : 2.237 ------------------------------------------------------------------------------- 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 430 ILE Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 476 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 72 THR 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 D residue 434 MET 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 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 120 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 152 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 239 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.067409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.050195 restraints weight = 58041.930| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.88 r_work: 0.2670 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3271 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 : 0.627 16.914 28533 Z= 0.301 Chirality : 0.045 0.441 3426 Planarity : 0.003 0.043 3477 Dihedral : 7.291 58.095 4479 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 2.48 % Allowed : 10.52 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2394 helix: 1.96 (0.28), residues: 396 sheet: -0.40 (0.18), residues: 819 loop : -1.01 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 571 HIS 0.006 0.001 HIS I 35B PHE 0.012 0.001 PHE D 53 TYR 0.021 0.001 TYR D 484 ARG 0.008 0.000 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 60) link_NAG-ASN : angle 3.02673 ( 180) link_ALPHA1-6 : bond 0.00621 ( 3) link_ALPHA1-6 : angle 1.52983 ( 9) link_BETA1-4 : bond 0.00477 ( 24) link_BETA1-4 : angle 1.44586 ( 72) link_ALPHA1-3 : bond 0.01064 ( 3) link_ALPHA1-3 : angle 1.56332 ( 9) hydrogen bonds : bond 0.03750 ( 692) hydrogen bonds : angle 4.84263 ( 1977) SS BOND : bond 0.00226 ( 42) SS BOND : angle 0.59988 ( 84) covalent geometry : bond 0.00410 (20760) covalent geometry : angle 0.57585 (28179) *********************** 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 284 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 2.337 Fit side-chains REVERT: E 475 MET cc_start: 0.9119 (mmm) cc_final: 0.8111 (mmm) REVERT: B 621 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8167 (tm-30) REVERT: B 632 ASP cc_start: 0.9337 (t70) cc_final: 0.8902 (t0) REVERT: H 46 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8190 (mt-10) REVERT: H 72 ASP cc_start: 0.8201 (t70) cc_final: 0.7270 (t0) REVERT: H 75 LYS cc_start: 0.9130 (mtmm) cc_final: 0.8690 (mtmm) REVERT: H 100 ASP cc_start: 0.8735 (t0) cc_final: 0.8347 (t0) REVERT: L 103 ARG cc_start: 0.7822 (ptm160) cc_final: 0.7417 (ptp-110) REVERT: D 36 VAL cc_start: 0.9360 (OUTLIER) cc_final: 0.9107 (p) REVERT: D 207 LYS cc_start: 0.7922 (tptp) cc_final: 0.7623 (tmtt) REVERT: A 621 GLU cc_start: 0.9020 (tt0) cc_final: 0.8380 (tm-30) REVERT: A 625 ASN cc_start: 0.9314 (t0) cc_final: 0.8664 (t0) REVERT: A 632 ASP cc_start: 0.9251 (t70) cc_final: 0.8960 (t0) REVERT: G 16 GLU cc_start: 0.8381 (pm20) cc_final: 0.7995 (pm20) REVERT: G 27 ASP cc_start: 0.9123 (t0) cc_final: 0.8585 (t0) REVERT: G 100 ASP cc_start: 0.8669 (t0) cc_final: 0.8383 (t0) REVERT: G 105 GLN cc_start: 0.9063 (pt0) cc_final: 0.8746 (pt0) REVERT: J 6 GLN cc_start: 0.8604 (mt0) cc_final: 0.8365 (mt0) REVERT: J 79 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8089 (mm-30) REVERT: J 100 GLN cc_start: 0.8886 (pm20) cc_final: 0.8552 (pm20) REVERT: F 166 ARG cc_start: 0.4543 (tpt170) cc_final: 0.1219 (tmt170) REVERT: C 621 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8070 (tm-30) REVERT: C 657 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8682 (tm-30) REVERT: C 659 ASP cc_start: 0.8833 (t0) cc_final: 0.8477 (m-30) REVERT: I 3 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7863 (mm-40) REVERT: I 5 GLN cc_start: 0.8555 (tp-100) cc_final: 0.8204 (tp40) REVERT: I 27 ASP cc_start: 0.9208 (t70) cc_final: 0.8917 (t0) REVERT: I 72 ASP cc_start: 0.8794 (t70) cc_final: 0.8385 (t0) REVERT: I 100 ASP cc_start: 0.8407 (t70) cc_final: 0.7980 (t70) REVERT: K 24 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8408 (mtp85) outliers start: 53 outliers final: 44 residues processed: 270 average time/residue: 0.3340 time to fit residues: 136.5702 Evaluate side-chains 266 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 220 time to evaluate : 2.025 ------------------------------------------------------------------------------- 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 635 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 120 VAL 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 D residue 434 MET Chi-restraints excluded: chain D residue 488 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 9 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 68 VAL Chi-restraints excluded: chain F residue 120 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 24 ARG 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 121 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 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 = 0.3196 r_free = 0.3196 target = 0.066766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.049485 restraints weight = 58020.753| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.88 r_work: 0.2656 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20892 Z= 0.205 Angle : 0.653 16.313 28533 Z= 0.314 Chirality : 0.046 0.429 3426 Planarity : 0.003 0.044 3477 Dihedral : 7.281 58.697 4479 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.86 % Rotamer: Outliers : 2.38 % Allowed : 11.27 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2394 helix: 1.92 (0.28), residues: 396 sheet: -0.40 (0.18), residues: 819 loop : -0.99 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 571 HIS 0.006 0.001 HIS I 35B PHE 0.013 0.001 PHE D 53 TYR 0.019 0.001 TYR D 484 ARG 0.006 0.000 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 60) link_NAG-ASN : angle 3.00107 ( 180) link_ALPHA1-6 : bond 0.00511 ( 3) link_ALPHA1-6 : angle 1.55668 ( 9) link_BETA1-4 : bond 0.00488 ( 24) link_BETA1-4 : angle 1.45076 ( 72) link_ALPHA1-3 : bond 0.00994 ( 3) link_ALPHA1-3 : angle 1.51415 ( 9) hydrogen bonds : bond 0.03909 ( 692) hydrogen bonds : angle 4.84801 ( 1977) SS BOND : bond 0.00269 ( 42) SS BOND : angle 0.66585 ( 84) covalent geometry : bond 0.00486 (20760) covalent geometry : angle 0.60515 (28179) *********************** 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 277 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 226 time to evaluate : 2.120 Fit side-chains REVERT: E 475 MET cc_start: 0.9130 (mmm) cc_final: 0.8119 (mmm) REVERT: B 621 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8148 (tm-30) REVERT: B 632 ASP cc_start: 0.9349 (t70) cc_final: 0.8911 (t0) REVERT: H 46 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8139 (mt-10) REVERT: H 72 ASP cc_start: 0.8224 (t70) cc_final: 0.7314 (t0) REVERT: H 75 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8707 (mtmm) REVERT: H 100 ASP cc_start: 0.8782 (t0) cc_final: 0.8390 (t0) REVERT: L 103 ARG cc_start: 0.7824 (ptm160) cc_final: 0.7417 (ptp-110) REVERT: D 150 MET cc_start: 0.8998 (tpt) cc_final: 0.8790 (tpp) REVERT: D 207 LYS cc_start: 0.7944 (tptp) cc_final: 0.7650 (tmtt) REVERT: D 475 MET cc_start: 0.8385 (mmm) cc_final: 0.7896 (mmt) REVERT: A 621 GLU cc_start: 0.9002 (tt0) cc_final: 0.8412 (tm-30) REVERT: A 625 ASN cc_start: 0.9304 (t0) cc_final: 0.8570 (t0) REVERT: G 16 GLU cc_start: 0.8352 (pm20) cc_final: 0.7988 (pm20) REVERT: G 27 ASP cc_start: 0.9164 (t0) cc_final: 0.8624 (t0) REVERT: G 100 ASP cc_start: 0.8673 (t0) cc_final: 0.8387 (t0) REVERT: G 105 GLN cc_start: 0.8892 (pt0) cc_final: 0.8639 (pt0) REVERT: J 79 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8118 (mm-30) REVERT: J 102 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7737 (t) REVERT: F 166 ARG cc_start: 0.4571 (tpt170) cc_final: 0.1057 (tmt170) REVERT: C 621 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8267 (tm-30) REVERT: C 657 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8702 (tm-30) REVERT: C 659 ASP cc_start: 0.8884 (t0) cc_final: 0.8515 (m-30) REVERT: I 27 ASP cc_start: 0.9201 (t70) cc_final: 0.8903 (t0) REVERT: I 72 ASP cc_start: 0.8806 (t70) cc_final: 0.8398 (t0) REVERT: I 100 ASP cc_start: 0.8456 (t70) cc_final: 0.8032 (t70) REVERT: K 24 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8420 (mtp85) outliers start: 51 outliers final: 44 residues processed: 266 average time/residue: 0.3405 time to fit residues: 138.0798 Evaluate side-chains 267 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 221 time to evaluate : 2.149 ------------------------------------------------------------------------------- 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 635 ILE Chi-restraints excluded: chain H residue 51 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 L residue 72 THR 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 D residue 434 MET Chi-restraints excluded: chain D residue 488 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 9 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 120 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 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 24 ARG 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 23 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 214 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.065746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.048469 restraints weight = 58537.332| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.88 r_work: 0.2627 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 20892 Z= 0.276 Angle : 0.709 15.926 28533 Z= 0.344 Chirality : 0.047 0.422 3426 Planarity : 0.004 0.046 3477 Dihedral : 7.466 59.634 4479 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.43 % Favored : 95.53 % Rotamer: Outliers : 2.57 % Allowed : 11.78 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2394 helix: 1.84 (0.28), residues: 396 sheet: -0.40 (0.18), residues: 813 loop : -1.11 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 571 HIS 0.006 0.001 HIS F 105 PHE 0.016 0.002 PHE I 91 TYR 0.019 0.001 TYR D 484 ARG 0.007 0.001 ARG J 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 60) link_NAG-ASN : angle 3.07246 ( 180) link_ALPHA1-6 : bond 0.00379 ( 3) link_ALPHA1-6 : angle 1.60778 ( 9) link_BETA1-4 : bond 0.00493 ( 24) link_BETA1-4 : angle 1.50782 ( 72) link_ALPHA1-3 : bond 0.00921 ( 3) link_ALPHA1-3 : angle 1.52569 ( 9) hydrogen bonds : bond 0.04221 ( 692) hydrogen bonds : angle 4.94572 ( 1977) SS BOND : bond 0.00310 ( 42) SS BOND : angle 0.80350 ( 84) covalent geometry : bond 0.00657 (20760) covalent geometry : angle 0.66278 (28179) *********************** 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 283 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 228 time to evaluate : 2.135 Fit side-chains REVERT: E 475 MET cc_start: 0.9135 (mmm) cc_final: 0.8157 (mmm) REVERT: B 621 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8174 (tm-30) REVERT: B 632 ASP cc_start: 0.9377 (t70) cc_final: 0.8939 (t0) REVERT: H 46 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8127 (mt-10) REVERT: H 72 ASP cc_start: 0.8230 (t70) cc_final: 0.7368 (t0) REVERT: H 75 LYS cc_start: 0.9146 (mtmm) cc_final: 0.8692 (mtmm) REVERT: H 100 ASP cc_start: 0.8807 (t0) cc_final: 0.8457 (t0) REVERT: D 166 ARG cc_start: 0.4829 (ttt-90) cc_final: 0.4548 (ttt-90) REVERT: D 207 LYS cc_start: 0.8028 (tptp) cc_final: 0.7664 (tptp) REVERT: A 621 GLU cc_start: 0.9001 (tt0) cc_final: 0.8411 (tm-30) REVERT: A 625 ASN cc_start: 0.9342 (t0) cc_final: 0.8655 (t0) REVERT: A 632 ASP cc_start: 0.9287 (t70) cc_final: 0.9014 (t0) REVERT: G 5 GLN cc_start: 0.8435 (tp-100) cc_final: 0.8074 (tp-100) REVERT: G 16 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7975 (pm20) REVERT: G 27 ASP cc_start: 0.9208 (t0) cc_final: 0.8948 (t0) REVERT: G 100 ASP cc_start: 0.8739 (t0) cc_final: 0.8442 (t0) REVERT: J 79 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8148 (mm-30) REVERT: J 102 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7757 (t) REVERT: F 166 ARG cc_start: 0.4645 (tpt170) cc_final: 0.0925 (tmt170) REVERT: C 621 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8247 (tm-30) REVERT: C 657 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8720 (tm-30) REVERT: I 3 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7780 (mm-40) REVERT: I 27 ASP cc_start: 0.9206 (t70) cc_final: 0.8920 (t0) REVERT: I 72 ASP cc_start: 0.8828 (t70) cc_final: 0.8423 (t0) REVERT: I 100 ILE cc_start: 0.9413 (mm) cc_final: 0.9205 (mm) REVERT: I 100 ASP cc_start: 0.8591 (t70) cc_final: 0.8170 (t70) REVERT: K 24 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7983 (tmm160) outliers start: 55 outliers final: 46 residues processed: 268 average time/residue: 0.3294 time to fit residues: 133.8556 Evaluate side-chains 271 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 222 time to evaluate : 2.151 ------------------------------------------------------------------------------- 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 635 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 72 THR 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 D residue 434 MET Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain A residue 513 VAL 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 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 9 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 120 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 24 ARG 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 82 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 125 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.067415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.049925 restraints weight = 57252.994| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.90 r_work: 0.2689 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20892 Z= 0.115 Angle : 0.624 17.271 28533 Z= 0.298 Chirality : 0.044 0.402 3426 Planarity : 0.003 0.042 3477 Dihedral : 7.041 59.715 4479 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.53 % Rotamer: Outliers : 2.06 % Allowed : 12.62 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2394 helix: 1.99 (0.28), residues: 396 sheet: -0.27 (0.18), residues: 816 loop : -0.98 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 571 HIS 0.006 0.001 HIS I 35B PHE 0.010 0.001 PHE D 53 TYR 0.020 0.001 TYR D 484 ARG 0.006 0.000 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 60) link_NAG-ASN : angle 2.94637 ( 180) link_ALPHA1-6 : bond 0.00497 ( 3) link_ALPHA1-6 : angle 1.41534 ( 9) link_BETA1-4 : bond 0.00508 ( 24) link_BETA1-4 : angle 1.28300 ( 72) link_ALPHA1-3 : bond 0.01054 ( 3) link_ALPHA1-3 : angle 1.22947 ( 9) hydrogen bonds : bond 0.03373 ( 692) hydrogen bonds : angle 4.69308 ( 1977) SS BOND : bond 0.00176 ( 42) SS BOND : angle 0.52908 ( 84) covalent geometry : bond 0.00265 (20760) covalent geometry : angle 0.57691 (28179) *********************** 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 284 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 2.110 Fit side-chains revert: symmetry clash REVERT: E 475 MET cc_start: 0.9094 (mmm) cc_final: 0.8028 (mmm) REVERT: B 621 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8076 (tm-30) REVERT: B 632 ASP cc_start: 0.9302 (t70) cc_final: 0.8819 (t0) REVERT: H 46 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8032 (mt-10) REVERT: H 95 GLU cc_start: 0.8986 (tt0) cc_final: 0.8713 (tt0) REVERT: H 100 ASP cc_start: 0.8746 (t0) cc_final: 0.8322 (t0) REVERT: D 166 ARG cc_start: 0.4730 (ttt-90) cc_final: 0.4454 (ttt-90) REVERT: D 207 LYS cc_start: 0.7903 (tptp) cc_final: 0.7622 (tmtt) REVERT: D 475 MET cc_start: 0.8307 (mmm) cc_final: 0.7803 (mmt) REVERT: A 625 ASN cc_start: 0.9277 (t0) cc_final: 0.8667 (t0) REVERT: A 632 ASP cc_start: 0.9219 (t70) cc_final: 0.8942 (t0) REVERT: G 5 GLN cc_start: 0.8562 (tp-100) cc_final: 0.8138 (tp-100) REVERT: G 16 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7968 (pm20) REVERT: G 27 ASP cc_start: 0.9143 (t0) cc_final: 0.8870 (t0) REVERT: G 100 ASP cc_start: 0.8554 (t0) cc_final: 0.8263 (t0) REVERT: J 79 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8098 (mm-30) REVERT: F 166 ARG cc_start: 0.4377 (tpt170) cc_final: 0.0715 (ttt-90) REVERT: F 415 THR cc_start: 0.9241 (OUTLIER) cc_final: 0.9027 (p) REVERT: C 621 GLU cc_start: 0.8525 (tm-30) cc_final: 0.7978 (tm-30) REVERT: C 659 ASP cc_start: 0.8729 (t0) cc_final: 0.8390 (m-30) REVERT: I 3 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7794 (mm-40) REVERT: I 27 ASP cc_start: 0.9197 (t70) cc_final: 0.8893 (t0) REVERT: I 72 ASP cc_start: 0.8796 (t70) cc_final: 0.8393 (t0) REVERT: I 100 ILE cc_start: 0.9376 (mm) cc_final: 0.9009 (mm) REVERT: I 100 ASP cc_start: 0.8346 (t70) cc_final: 0.7888 (t70) outliers start: 44 outliers final: 37 residues processed: 273 average time/residue: 0.3287 time to fit residues: 136.3568 Evaluate side-chains 267 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 228 time to evaluate : 2.206 ------------------------------------------------------------------------------- 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 635 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 38 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 D residue 434 MET Chi-restraints excluded: chain A residue 608 VAL 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 9 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 120 VAL Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 415 THR 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 I residue 89 VAL 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 229 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.067459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.050331 restraints weight = 57617.282| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.86 r_work: 0.2677 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20892 Z= 0.152 Angle : 0.632 16.506 28533 Z= 0.303 Chirality : 0.045 0.393 3426 Planarity : 0.003 0.043 3477 Dihedral : 6.990 57.439 4479 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 1.96 % Allowed : 12.86 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2394 helix: 2.00 (0.28), residues: 396 sheet: -0.24 (0.18), residues: 816 loop : -0.97 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 571 HIS 0.005 0.001 HIS I 35B PHE 0.010 0.001 PHE I 91 TYR 0.026 0.001 TYR D 484 ARG 0.005 0.000 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 60) link_NAG-ASN : angle 2.88140 ( 180) link_ALPHA1-6 : bond 0.00391 ( 3) link_ALPHA1-6 : angle 1.53437 ( 9) link_BETA1-4 : bond 0.00492 ( 24) link_BETA1-4 : angle 1.35913 ( 72) link_ALPHA1-3 : bond 0.00916 ( 3) link_ALPHA1-3 : angle 1.31238 ( 9) hydrogen bonds : bond 0.03497 ( 692) hydrogen bonds : angle 4.66393 ( 1977) SS BOND : bond 0.00207 ( 42) SS BOND : angle 0.57629 ( 84) covalent geometry : bond 0.00358 (20760) covalent geometry : angle 0.58708 (28179) ********************** 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 274 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 2.443 Fit side-chains REVERT: E 475 MET cc_start: 0.9133 (mmm) cc_final: 0.8109 (mmm) REVERT: B 621 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8193 (tm-30) REVERT: B 632 ASP cc_start: 0.9332 (t70) cc_final: 0.8854 (t0) REVERT: H 46 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8068 (mt-10) REVERT: H 75 LYS cc_start: 0.9256 (mtmm) cc_final: 0.8892 (mtmm) REVERT: H 95 GLU cc_start: 0.8978 (tt0) cc_final: 0.8716 (tt0) REVERT: H 100 ASP cc_start: 0.8775 (t0) cc_final: 0.8349 (t0) REVERT: D 166 ARG cc_start: 0.4744 (ttt-90) cc_final: 0.4468 (ttt-90) REVERT: D 207 LYS cc_start: 0.7922 (tptp) cc_final: 0.7657 (tmtt) REVERT: D 475 MET cc_start: 0.8421 (mmm) cc_final: 0.7958 (mmt) REVERT: A 625 ASN cc_start: 0.9298 (t0) cc_final: 0.8698 (t0) REVERT: A 632 ASP cc_start: 0.9241 (t70) cc_final: 0.8963 (t0) REVERT: G 16 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: G 27 ASP cc_start: 0.9155 (t0) cc_final: 0.8883 (t0) REVERT: G 100 ASP cc_start: 0.8576 (t0) cc_final: 0.8304 (t0) REVERT: J 79 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8118 (mm-30) REVERT: F 166 ARG cc_start: 0.4503 (tpt170) cc_final: 0.1101 (tmt170) REVERT: C 621 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8087 (tm-30) REVERT: C 659 ASP cc_start: 0.8765 (t0) cc_final: 0.8435 (m-30) REVERT: I 3 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7828 (mm-40) REVERT: I 27 ASP cc_start: 0.9207 (t70) cc_final: 0.8895 (t0) REVERT: I 72 ASP cc_start: 0.8815 (t70) cc_final: 0.8412 (t0) REVERT: I 100 ILE cc_start: 0.9399 (mm) cc_final: 0.9087 (mm) REVERT: I 100 ASP cc_start: 0.8399 (t70) cc_final: 0.7968 (t70) outliers start: 42 outliers final: 39 residues processed: 262 average time/residue: 0.3385 time to fit residues: 135.1858 Evaluate side-chains 266 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 2.113 ------------------------------------------------------------------------------- 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 635 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 38 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 D residue 434 MET 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 9 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 120 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 I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 89 VAL 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 196 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 234 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** D 398 ASN ** A 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** 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 = 0.3214 r_free = 0.3214 target = 0.067598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.050447 restraints weight = 57819.275| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.88 r_work: 0.2679 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20892 Z= 0.146 Angle : 0.627 16.450 28533 Z= 0.301 Chirality : 0.044 0.385 3426 Planarity : 0.003 0.042 3477 Dihedral : 6.913 56.841 4479 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 1.96 % Allowed : 13.04 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2394 helix: 2.01 (0.28), residues: 396 sheet: -0.21 (0.18), residues: 816 loop : -0.97 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 571 HIS 0.005 0.001 HIS I 35B PHE 0.010 0.001 PHE D 53 TYR 0.026 0.001 TYR D 484 ARG 0.005 0.000 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 60) link_NAG-ASN : angle 2.86530 ( 180) link_ALPHA1-6 : bond 0.00412 ( 3) link_ALPHA1-6 : angle 1.53378 ( 9) link_BETA1-4 : bond 0.00503 ( 24) link_BETA1-4 : angle 1.34444 ( 72) link_ALPHA1-3 : bond 0.00897 ( 3) link_ALPHA1-3 : angle 1.27277 ( 9) hydrogen bonds : bond 0.03443 ( 692) hydrogen bonds : angle 4.63581 ( 1977) SS BOND : bond 0.00201 ( 42) SS BOND : angle 0.56227 ( 84) covalent geometry : bond 0.00345 (20760) covalent geometry : angle 0.58188 (28179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12480.82 seconds wall clock time: 218 minutes 56.84 seconds (13136.84 seconds total)