Starting phenix.real_space_refine on Sun Oct 12 03:19:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8to7_41438/10_2025/8to7_41438.cif Found real_map, /net/cci-nas-00/data/ceres_data/8to7_41438/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8to7_41438/10_2025/8to7_41438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8to7_41438/10_2025/8to7_41438.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8to7_41438/10_2025/8to7_41438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8to7_41438/10_2025/8to7_41438.map" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 12738 2.51 5 N 3423 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20361 Number of models: 1 Model: "" Number of chains: 33 Chain: "E" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "H" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "A" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "G" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "J" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "C" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "K" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.04, per 1000 atoms: 0.25 Number of scatterers: 20361 At special positions: 0 Unit cell: (132.72, 139.02, 136.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4080 8.00 N 3423 7.00 C 12738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 433 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.04 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS A 605 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " " BMA U 3 " - " MAN U 5 " " BMA Z 3 " - " MAN Z 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG A 701 " - " ASN A 618 " " NAG A 702 " - " ASN A 611 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 611 " " NAG C 701 " - " ASN C 618 " " NAG C 702 " - " ASN C 611 " " NAG D 601 " - " ASN D 133 " " NAG D 602 " - " ASN D 197 " " NAG D 603 " - " ASN D 234 " " NAG D 604 " - " ASN D 276 " " NAG D 605 " - " ASN D 295 " " NAG D 606 " - " ASN D 301 " " NAG D 607 " - " ASN D 332 " " NAG D 608 " - " ASN D 339 " " NAG D 609 " - " ASN D 355 " " NAG D 610 " - " ASN D 363 " " NAG D 611 " - " ASN D 386 " " NAG D 612 " - " ASN D 392 " " NAG D 613 " - " ASN D 448 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 197 " " NAG E 603 " - " ASN E 234 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 295 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 332 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 355 " " NAG E 610 " - " ASN E 363 " " NAG E 611 " - " ASN E 386 " " NAG E 612 " - " ASN E 392 " " NAG E 613 " - " ASN E 448 " " NAG F 601 " - " ASN F 133 " " NAG F 602 " - " ASN F 197 " " NAG F 603 " - " ASN F 234 " " NAG F 604 " - " ASN F 276 " " NAG F 605 " - " ASN F 295 " " NAG F 606 " - " ASN F 301 " " NAG F 607 " - " ASN F 332 " " NAG F 608 " - " ASN F 339 " " NAG F 609 " - " ASN F 355 " " NAG F 610 " - " ASN F 363 " " NAG F 611 " - " ASN F 386 " " NAG F 612 " - " ASN F 392 " " NAG F 613 " - " ASN F 448 " " NAG M 1 " - " ASN E 88 " " NAG N 1 " - " ASN E 156 " " NAG O 1 " - " ASN E 160 " " NAG P 1 " - " ASN E 262 " " NAG Q 1 " - " ASN B 637 " " NAG R 1 " - " ASN D 88 " " NAG S 1 " - " ASN D 156 " " NAG T 1 " - " ASN D 160 " " NAG U 1 " - " ASN D 262 " " NAG V 1 " - " ASN A 637 " " NAG W 1 " - " ASN F 88 " " NAG X 1 " - " ASN F 156 " " NAG Y 1 " - " ASN F 160 " " NAG Z 1 " - " ASN F 262 " " NAG a 1 " - " ASN C 637 " Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 797.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4506 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 42 sheets defined 19.3% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'E' and resid 98 through 115 removed outlier: 4.452A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.743A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 126' Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.057A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.573A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.918A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.529A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 626 removed outlier: 3.570A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.638A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.151A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 116 removed outlier: 4.525A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.566A pdb=" N LEU D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS D 126 " --> pdb=" O THR D 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 126' Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 351 removed outlier: 4.293A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 475 through 481 removed outlier: 3.515A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 4.090A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 596 removed outlier: 3.505A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 615 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 662 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'F' and resid 98 through 115 removed outlier: 4.481A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.885A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.512A pdb=" N THR F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 390 Processing helix chain 'F' and resid 475 through 481 removed outlier: 3.724A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 527 removed outlier: 4.278A pdb=" N GLY C 527 " --> pdb=" O GLY C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 542 removed outlier: 4.168A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 596 removed outlier: 3.619A pdb=" N TRP C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 615 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 636 Processing helix chain 'C' and resid 638 through 664 removed outlier: 3.914A pdb=" N LEU C 663 " --> pdb=" O ASP C 659 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.470A pdb=" N VAL B 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL E 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR B 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N TYR E 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N CYS B 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.082A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.502A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE E 53 " --> pdb=" O CYS E 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.946A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.785A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.938A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.223A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.300A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.430A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.898A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.189A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 359 through 361 Processing sheet with id=AA7, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.189A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.898A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.430A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.300A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.223A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 413 through 420 removed outlier: 3.725A pdb=" N PHE E 383 " --> pdb=" O PHE E 376 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.571A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.511A pdb=" N PHE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.531A pdb=" N LEU H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR H 35 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP H 35A" --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ARG H 38 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLY H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.252A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.252A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AB6, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.582A pdb=" N LYS D 487 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 75 through 76 removed outlier: 3.527A pdb=" N PHE D 53 " --> pdb=" O CYS D 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.689A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 169 through 177 removed outlier: 3.757A pdb=" N LYS D 189 " --> pdb=" O CYS D 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.586A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 271 through 273 removed outlier: 3.670A pdb=" N ILE D 443 " --> pdb=" O ARG D 298 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS D 330 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU D 381 " --> pdb=" O CYS D 378 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.603A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.564A pdb=" N GLN G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AC6, first strand: chain 'G' and resid 57 through 59 removed outlier: 3.575A pdb=" N GLY G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL G 89 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 57 through 59 removed outlier: 3.575A pdb=" N GLY G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL G 89 " --> pdb=" O GLN G 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.542A pdb=" N ALA J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP J 70 " --> pdb=" O ALA J 67 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.952A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU J 33 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.952A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 494 through 499 removed outlier: 6.174A pdb=" N VAL C 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N VAL F 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR C 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N TYR F 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N CYS C 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.181A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.713A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER F 56 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE F 53 " --> pdb=" O CYS F 218 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 91 through 93 removed outlier: 3.566A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY F 237 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 169 through 177 removed outlier: 3.583A pdb=" N LYS F 189 " --> pdb=" O CYS F 131 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.357A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 259 through 261 removed outlier: 3.736A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE F 376 " --> pdb=" O PHE F 383 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 271 through 273 removed outlier: 3.562A pdb=" N MET F 271 " --> pdb=" O GLN F 287 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE F 359 " --> pdb=" O TRP F 395 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 304 through 312 removed outlier: 3.565A pdb=" N ILE F 309 " --> pdb=" O GLN F 315 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.592A pdb=" N ALA I 88 " --> pdb=" O VAL I 109 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TRP I 35A" --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYR I 50 " --> pdb=" O TRP I 35A" (cutoff:3.500A) removed outlier: 7.287A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY I 44 " --> pdb=" O SER I 40 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.592A pdb=" N ALA I 88 " --> pdb=" O VAL I 109 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG I 96 " --> pdb=" O VAL I 100G" (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL I 100G" --> pdb=" O ARG I 96 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.635A pdb=" N ALA K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.892A pdb=" N ASP K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL K 104 " --> pdb=" O GLY K 84 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU K 33 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 1977 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 2.10 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: 43.860 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: 0.030 Extract box with map and model: 1.110 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.990 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20892 Z= 0.334 Angle : 1.123 16.234 28533 Z= 0.583 Chirality : 0.069 0.927 3426 Planarity : 0.006 0.265 3477 Dihedral : 15.433 108.794 8973 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.17), residues: 2394 helix: 1.43 (0.28), residues: 393 sheet: -1.01 (0.19), residues: 699 loop : -0.99 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 308 TYR 0.034 0.002 TYR D 486 PHE 0.018 0.002 PHE E 233 TRP 0.049 0.002 TRP D 427 HIS 0.025 0.002 HIS I 35B Details of bonding type rmsd covalent geometry : bond 0.00628 (20760) covalent geometry : angle 1.09252 (28179) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.30042 ( 84) hydrogen bonds : bond 0.23818 ( 692) hydrogen bonds : angle 8.29025 ( 1977) link_ALPHA1-3 : bond 0.00570 ( 3) link_ALPHA1-3 : angle 1.20891 ( 9) link_ALPHA1-6 : bond 0.00231 ( 3) link_ALPHA1-6 : angle 1.52907 ( 9) link_BETA1-4 : bond 0.00928 ( 24) link_BETA1-4 : angle 2.38653 ( 72) link_NAG-ASN : bond 0.00471 ( 60) link_NAG-ASN : angle 3.13279 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.822 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: 0.8947 (t0) REVERT: I 72 ASP cc_start: 0.8739 (t70) cc_final: 0.8332 (t0) REVERT: I 95 GLU cc_start: 0.8059 (pt0) cc_final: 0.7751 (pt0) REVERT: I 100 ILE cc_start: 0.8715 (mm) cc_final: 0.8295 (mm) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1492 time to fit residues: 67.7664 Evaluate side-chains 236 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.0010 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN ** J 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN C 607 ASN C 653 GLN K 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.074262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.057172 restraints weight = 56738.627| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 4.02 r_work: 0.2790 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20892 Z= 0.115 Angle : 0.640 12.747 28533 Z= 0.313 Chirality : 0.047 0.471 3426 Planarity : 0.004 0.054 3477 Dihedral : 11.059 79.462 4479 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.98 % Allowed : 5.70 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.17), residues: 2394 helix: 1.59 (0.28), residues: 405 sheet: -0.68 (0.18), residues: 783 loop : -0.87 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 588 TYR 0.014 0.001 TYR D 484 PHE 0.011 0.001 PHE D 383 TRP 0.018 0.001 TRP B 571 HIS 0.009 0.001 HIS G 35B Details of bonding type rmsd covalent geometry : bond 0.00246 (20760) covalent geometry : angle 0.59554 (28179) SS BOND : bond 0.00241 ( 42) SS BOND : angle 0.64890 ( 84) hydrogen bonds : bond 0.04526 ( 692) hydrogen bonds : angle 6.01254 ( 1977) link_ALPHA1-3 : bond 0.00914 ( 3) link_ALPHA1-3 : angle 2.35662 ( 9) link_ALPHA1-6 : bond 0.00372 ( 3) link_ALPHA1-6 : angle 1.89133 ( 9) link_BETA1-4 : bond 0.00784 ( 24) link_BETA1-4 : angle 2.09395 ( 72) link_NAG-ASN : bond 0.00395 ( 60) link_NAG-ASN : angle 2.64422 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 253 time to evaluate : 0.852 Fit side-chains REVERT: E 161 MET cc_start: 0.8674 (tpt) cc_final: 0.8427 (tpt) REVERT: E 462 ASN cc_start: 0.7991 (t0) cc_final: 0.7779 (t0) REVERT: B 625 ASN cc_start: 0.9072 (t0) cc_final: 0.8502 (t0) REVERT: H 6 GLU cc_start: 0.8580 (mp0) cc_final: 0.8281 (mp0) REVERT: H 16 GLU cc_start: 0.8579 (pm20) cc_final: 0.8354 (pm20) REVERT: H 46 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8215 (mt-10) REVERT: H 72 ASP cc_start: 0.7967 (t70) cc_final: 0.7304 (t0) REVERT: H 75 LYS cc_start: 0.8965 (mtmm) cc_final: 0.8705 (mtmm) REVERT: H 105 GLN cc_start: 0.8952 (pt0) cc_final: 0.8696 (pt0) REVERT: L 79 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7218 (mm-30) REVERT: L 103 ARG cc_start: 0.7588 (ptm160) cc_final: 0.7105 (ptp-110) REVERT: A 621 GLU cc_start: 0.8793 (tt0) cc_final: 0.7926 (tm-30) REVERT: A 625 ASN cc_start: 0.9129 (t0) cc_final: 0.8392 (t0) REVERT: G 3 GLN cc_start: 0.8481 (mm110) cc_final: 0.8276 (mm110) REVERT: G 16 GLU cc_start: 0.8165 (pm20) cc_final: 0.7576 (pm20) REVERT: G 72 ASP cc_start: 0.7953 (p0) cc_final: 0.7605 (p0) REVERT: G 100 ASP cc_start: 0.8371 (t0) cc_final: 0.8081 (t0) REVERT: J 79 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7455 (mm-30) REVERT: J 82 ASP cc_start: 0.7811 (m-30) cc_final: 0.7339 (m-30) REVERT: J 100 GLN cc_start: 0.8777 (pm20) cc_final: 0.8471 (pm20) REVERT: F 166 ARG cc_start: 0.4381 (tpt170) cc_final: 0.3360 (tpt170) REVERT: F 475 MET cc_start: 0.8745 (tpp) cc_final: 0.8229 (mmt) REVERT: I 5 GLN cc_start: 0.8491 (tp-100) cc_final: 0.8067 (tp40) REVERT: I 27 ASP cc_start: 0.9289 (t70) cc_final: 0.8947 (t0) REVERT: I 72 ASP cc_start: 0.8693 (t70) cc_final: 0.8378 (t0) REVERT: I 95 GLU cc_start: 0.8529 (pt0) cc_final: 0.8328 (pt0) REVERT: I 100 ILE cc_start: 0.8802 (mm) cc_final: 0.8350 (mm) REVERT: K 82 ASP cc_start: 0.7651 (m-30) cc_final: 0.7314 (m-30) outliers start: 21 outliers final: 17 residues processed: 266 average time/residue: 0.1531 time to fit residues: 61.6857 Evaluate side-chains 249 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 83 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 183 optimal weight: 6.9990 chunk 169 optimal weight: 0.0970 chunk 225 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 overall best weight: 2.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 377 ASN H 39 GLN F 352 HIS ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.068367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.050205 restraints weight = 57750.871| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.94 r_work: 0.2604 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20892 Z= 0.213 Angle : 0.669 11.782 28533 Z= 0.327 Chirality : 0.048 0.475 3426 Planarity : 0.004 0.048 3477 Dihedral : 8.530 66.158 4479 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.64 % Allowed : 7.15 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.17), residues: 2394 helix: 1.85 (0.28), residues: 396 sheet: -0.47 (0.18), residues: 786 loop : -0.89 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 94 TYR 0.015 0.002 TYR D 484 PHE 0.019 0.002 PHE H 78 TRP 0.023 0.002 TRP F 479 HIS 0.005 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00506 (20760) covalent geometry : angle 0.63019 (28179) SS BOND : bond 0.00278 ( 42) SS BOND : angle 0.78920 ( 84) hydrogen bonds : bond 0.04402 ( 692) hydrogen bonds : angle 5.30391 ( 1977) link_ALPHA1-3 : bond 0.01006 ( 3) link_ALPHA1-3 : angle 1.86820 ( 9) link_ALPHA1-6 : bond 0.00465 ( 3) link_ALPHA1-6 : angle 1.81152 ( 9) link_BETA1-4 : bond 0.00608 ( 24) link_BETA1-4 : angle 1.93475 ( 72) link_NAG-ASN : bond 0.00356 ( 60) link_NAG-ASN : angle 2.57692 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 1.036 Fit side-chains REVERT: E 434 MET cc_start: 0.8865 (ttp) cc_final: 0.8641 (ttt) REVERT: E 475 MET cc_start: 0.8991 (mmm) cc_final: 0.7653 (mmm) REVERT: B 621 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7901 (tm-30) REVERT: B 625 ASN cc_start: 0.9016 (t0) cc_final: 0.8431 (t0) REVERT: B 632 ASP cc_start: 0.9132 (t0) cc_final: 0.8820 (t0) REVERT: H 27 ASP cc_start: 0.9247 (t0) cc_final: 0.9021 (t0) REVERT: H 46 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8150 (mt-10) REVERT: H 72 ASP cc_start: 0.7891 (t70) cc_final: 0.7126 (t0) REVERT: H 75 LYS cc_start: 0.8995 (mtmm) cc_final: 0.8501 (mtmm) REVERT: H 100 TYR cc_start: 0.8739 (m-80) cc_final: 0.8268 (m-80) REVERT: H 100 ASP cc_start: 0.8503 (t0) cc_final: 0.8140 (t0) REVERT: L 79 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7611 (mm-30) REVERT: L 103 ARG cc_start: 0.7530 (ptm160) cc_final: 0.7097 (ptp-110) REVERT: A 621 GLU cc_start: 0.9014 (tt0) cc_final: 0.8271 (tm-30) REVERT: A 625 ASN cc_start: 0.9289 (t0) cc_final: 0.8680 (t0) REVERT: G 16 GLU cc_start: 0.8334 (pm20) cc_final: 0.7706 (pm20) REVERT: G 27 ASP cc_start: 0.9037 (t0) cc_final: 0.8836 (t0) REVERT: G 100 ASP cc_start: 0.8746 (t0) cc_final: 0.8325 (t0) REVERT: J 79 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7721 (mm-30) REVERT: J 100 GLN cc_start: 0.8692 (pm20) cc_final: 0.8474 (pm20) REVERT: F 166 ARG cc_start: 0.4519 (tpt170) cc_final: 0.1512 (tmt170) REVERT: C 621 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7915 (tm-30) REVERT: C 659 ASP cc_start: 0.8662 (t0) cc_final: 0.8245 (m-30) REVERT: I 3 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7939 (mm110) REVERT: I 5 GLN cc_start: 0.8453 (tp-100) cc_final: 0.8085 (tp40) REVERT: I 16 GLU cc_start: 0.8309 (pm20) cc_final: 0.7976 (pm20) REVERT: I 27 ASP cc_start: 0.9294 (t70) cc_final: 0.8813 (t70) REVERT: I 72 ASP cc_start: 0.8612 (t70) cc_final: 0.8176 (t0) REVERT: I 100 ILE cc_start: 0.9095 (mm) cc_final: 0.8858 (mm) REVERT: I 100 ASP cc_start: 0.8387 (t0) cc_final: 0.8110 (t70) REVERT: K 24 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7612 (tmm160) outliers start: 35 outliers final: 27 residues processed: 269 average time/residue: 0.1730 time to fit residues: 70.3201 Evaluate side-chains 251 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 97 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 80 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 1 ASP Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 58 VAL 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 184 optimal weight: 0.0050 chunk 103 optimal weight: 6.9990 chunk 124 optimal weight: 0.3980 chunk 183 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 227 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** J 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN C 653 GLN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.071893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.054430 restraints weight = 57218.032| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.97 r_work: 0.2823 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20892 Z= 0.118 Angle : 0.601 11.726 28533 Z= 0.289 Chirality : 0.046 0.515 3426 Planarity : 0.003 0.043 3477 Dihedral : 7.753 59.206 4479 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.36 % Allowed : 8.60 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.17), residues: 2394 helix: 1.99 (0.28), residues: 396 sheet: -0.36 (0.18), residues: 786 loop : -0.85 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 588 TYR 0.012 0.001 TYR F 173 PHE 0.011 0.001 PHE H 78 TRP 0.015 0.001 TRP F 479 HIS 0.009 0.001 HIS I 35B Details of bonding type rmsd covalent geometry : bond 0.00270 (20760) covalent geometry : angle 0.55610 (28179) SS BOND : bond 0.00185 ( 42) SS BOND : angle 0.50043 ( 84) hydrogen bonds : bond 0.03670 ( 692) hydrogen bonds : angle 5.04042 ( 1977) link_ALPHA1-3 : bond 0.01041 ( 3) link_ALPHA1-3 : angle 1.83137 ( 9) link_ALPHA1-6 : bond 0.00724 ( 3) link_ALPHA1-6 : angle 1.70151 ( 9) link_BETA1-4 : bond 0.00485 ( 24) link_BETA1-4 : angle 1.66586 ( 72) link_NAG-ASN : bond 0.00454 ( 60) link_NAG-ASN : angle 2.71986 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: E 166 ARG cc_start: 0.5301 (ttt-90) cc_final: 0.4792 (ttt-90) REVERT: E 475 MET cc_start: 0.9087 (mmm) cc_final: 0.8469 (mmm) REVERT: B 613 SER cc_start: 0.9558 (m) cc_final: 0.9334 (t) REVERT: B 621 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 625 ASN cc_start: 0.9097 (t0) cc_final: 0.8439 (t0) REVERT: B 632 ASP cc_start: 0.9306 (t0) cc_final: 0.8925 (t0) REVERT: H 46 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8277 (mt-10) REVERT: H 72 ASP cc_start: 0.8256 (t70) cc_final: 0.7382 (t0) REVERT: H 75 LYS cc_start: 0.9093 (mtmm) cc_final: 0.8745 (mtmm) REVERT: H 100 TYR cc_start: 0.8965 (m-80) cc_final: 0.8692 (m-80) REVERT: H 100 ASP cc_start: 0.8439 (t0) cc_final: 0.8103 (t0) REVERT: L 79 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8050 (mm-30) REVERT: L 103 ARG cc_start: 0.7879 (ptm160) cc_final: 0.7423 (ptp-110) REVERT: A 621 GLU cc_start: 0.9039 (tt0) cc_final: 0.8431 (tm-30) REVERT: A 625 ASN cc_start: 0.9230 (t0) cc_final: 0.8612 (t0) REVERT: A 633 LYS cc_start: 0.9191 (mttt) cc_final: 0.8988 (mttm) REVERT: G 16 GLU cc_start: 0.8419 (pm20) cc_final: 0.7732 (pm20) REVERT: G 27 ASP cc_start: 0.9027 (t0) cc_final: 0.8763 (t0) REVERT: G 72 ASP cc_start: 0.8212 (p0) cc_final: 0.7883 (p0) REVERT: G 100 ASP cc_start: 0.8586 (t0) cc_final: 0.8241 (t0) REVERT: J 6 GLN cc_start: 0.8573 (mt0) cc_final: 0.8149 (mt0) REVERT: J 79 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7924 (mm-30) REVERT: J 100 GLN cc_start: 0.8833 (pm20) cc_final: 0.8411 (pm20) REVERT: F 166 ARG cc_start: 0.4666 (tpt170) cc_final: 0.2801 (tpt170) REVERT: C 621 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8138 (tm-30) REVERT: C 632 ASP cc_start: 0.9188 (t70) cc_final: 0.8845 (t0) REVERT: C 659 ASP cc_start: 0.8824 (t0) cc_final: 0.8481 (m-30) REVERT: I 3 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8052 (mm-40) REVERT: I 5 GLN cc_start: 0.8522 (tp-100) cc_final: 0.8148 (tp40) REVERT: I 27 ASP cc_start: 0.9198 (t70) cc_final: 0.8941 (t0) REVERT: I 72 ASP cc_start: 0.8754 (t70) cc_final: 0.8351 (t0) REVERT: I 100 ASP cc_start: 0.8299 (t0) cc_final: 0.8028 (t70) REVERT: K 24 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7748 (tmm160) outliers start: 29 outliers final: 22 residues processed: 261 average time/residue: 0.1585 time to fit residues: 62.1208 Evaluate side-chains 248 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 430 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 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 136 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 239 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.048739 restraints weight = 59463.432| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 4.06 r_work: 0.2594 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20892 Z= 0.236 Angle : 0.682 15.164 28533 Z= 0.331 Chirality : 0.047 0.464 3426 Planarity : 0.004 0.051 3477 Dihedral : 7.628 59.919 4479 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 2.38 % Allowed : 8.93 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.17), residues: 2394 helix: 1.71 (0.28), residues: 405 sheet: -0.40 (0.18), residues: 816 loop : -0.99 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 94 TYR 0.015 0.001 TYR D 484 PHE 0.016 0.002 PHE H 78 TRP 0.016 0.001 TRP B 571 HIS 0.008 0.001 HIS I 35B Details of bonding type rmsd covalent geometry : bond 0.00562 (20760) covalent geometry : angle 0.63434 (28179) SS BOND : bond 0.00276 ( 42) SS BOND : angle 0.76834 ( 84) hydrogen bonds : bond 0.04232 ( 692) hydrogen bonds : angle 5.04328 ( 1977) link_ALPHA1-3 : bond 0.01032 ( 3) link_ALPHA1-3 : angle 1.81987 ( 9) link_ALPHA1-6 : bond 0.00530 ( 3) link_ALPHA1-6 : angle 1.59298 ( 9) link_BETA1-4 : bond 0.00512 ( 24) link_BETA1-4 : angle 1.63007 ( 72) link_NAG-ASN : bond 0.00435 ( 60) link_NAG-ASN : angle 3.00307 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 232 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: E 166 ARG cc_start: 0.5352 (ttt-90) cc_final: 0.4250 (ttt-90) REVERT: B 613 SER cc_start: 0.9527 (m) cc_final: 0.9286 (t) REVERT: B 625 ASN cc_start: 0.9071 (t0) cc_final: 0.8822 (m-40) REVERT: B 632 ASP cc_start: 0.9285 (t70) cc_final: 0.8877 (t0) REVERT: H 46 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8331 (mt-10) REVERT: H 72 ASP cc_start: 0.8092 (t70) cc_final: 0.7260 (t0) REVERT: H 75 LYS cc_start: 0.9078 (mtmm) cc_final: 0.8663 (mtmm) REVERT: H 100 ASP cc_start: 0.8634 (t0) cc_final: 0.8194 (t0) REVERT: L 79 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7937 (mm-30) REVERT: L 81 GLU cc_start: 0.8484 (pm20) cc_final: 0.8230 (pp20) REVERT: L 103 ARG cc_start: 0.7711 (ptm160) cc_final: 0.7316 (ptp-110) REVERT: D 166 ARG cc_start: 0.4814 (ttt-90) cc_final: 0.4476 (ttt-90) REVERT: A 621 GLU cc_start: 0.9070 (tt0) cc_final: 0.8353 (tm-30) REVERT: A 625 ASN cc_start: 0.9306 (t0) cc_final: 0.8581 (t0) REVERT: A 632 ASP cc_start: 0.9269 (OUTLIER) cc_final: 0.8968 (t0) REVERT: G 5 GLN cc_start: 0.8614 (tp-100) cc_final: 0.8323 (tp-100) REVERT: G 16 GLU cc_start: 0.8351 (pm20) cc_final: 0.7941 (pm20) REVERT: G 27 ASP cc_start: 0.9087 (t0) cc_final: 0.8766 (t0) REVERT: G 100 ASP cc_start: 0.8773 (t0) cc_final: 0.8388 (t0) REVERT: J 79 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8007 (mm-30) REVERT: J 82 ASP cc_start: 0.8460 (m-30) cc_final: 0.8191 (m-30) REVERT: J 100 GLN cc_start: 0.8753 (pm20) cc_final: 0.8516 (pm20) REVERT: F 166 ARG cc_start: 0.4654 (tpt170) cc_final: 0.1581 (tmt170) REVERT: C 621 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8086 (tm-30) REVERT: C 657 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8677 (tm-30) REVERT: I 5 GLN cc_start: 0.8544 (tp-100) cc_final: 0.8181 (tp40) REVERT: I 27 ASP cc_start: 0.9250 (t70) cc_final: 0.8947 (t0) REVERT: I 72 ASP cc_start: 0.8732 (t70) cc_final: 0.8280 (t0) REVERT: K 24 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7871 (tmm160) outliers start: 51 outliers final: 39 residues processed: 265 average time/residue: 0.1685 time to fit residues: 67.5587 Evaluate side-chains 258 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 217 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 12 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 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 51 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 218 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 302 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.066627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.049354 restraints weight = 57818.015| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.86 r_work: 0.2649 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 20892 Z= 0.246 Angle : 0.680 15.690 28533 Z= 0.329 Chirality : 0.047 0.453 3426 Planarity : 0.004 0.042 3477 Dihedral : 7.551 59.754 4479 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 2.34 % Allowed : 10.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.17), residues: 2394 helix: 1.66 (0.28), residues: 405 sheet: -0.34 (0.18), residues: 807 loop : -1.01 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 476 TYR 0.020 0.001 TYR D 484 PHE 0.015 0.002 PHE H 78 TRP 0.021 0.001 TRP B 571 HIS 0.007 0.001 HIS I 35B Details of bonding type rmsd covalent geometry : bond 0.00584 (20760) covalent geometry : angle 0.63111 (28179) SS BOND : bond 0.00275 ( 42) SS BOND : angle 0.72803 ( 84) hydrogen bonds : bond 0.04139 ( 692) hydrogen bonds : angle 4.98289 ( 1977) link_ALPHA1-3 : bond 0.00898 ( 3) link_ALPHA1-3 : angle 1.59936 ( 9) link_ALPHA1-6 : bond 0.00518 ( 3) link_ALPHA1-6 : angle 1.57512 ( 9) link_BETA1-4 : bond 0.00497 ( 24) link_BETA1-4 : angle 1.47852 ( 72) link_NAG-ASN : bond 0.00590 ( 60) link_NAG-ASN : angle 3.09465 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 0.794 Fit side-chains REVERT: E 166 ARG cc_start: 0.5415 (ttt-90) cc_final: 0.4374 (ttt-90) REVERT: B 621 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8222 (tm-30) REVERT: B 625 ASN cc_start: 0.9108 (t0) cc_final: 0.8898 (m-40) REVERT: B 632 ASP cc_start: 0.9346 (t70) cc_final: 0.8964 (t0) REVERT: H 46 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8276 (mt-10) REVERT: H 72 ASP cc_start: 0.8218 (t70) cc_final: 0.7338 (t0) REVERT: H 75 LYS cc_start: 0.9125 (mtmm) cc_final: 0.8682 (mtmm) REVERT: H 100 ASP cc_start: 0.8669 (t0) cc_final: 0.8246 (t0) REVERT: L 79 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7993 (mm-30) REVERT: L 103 ARG cc_start: 0.7837 (ptm160) cc_final: 0.7431 (ptp-110) REVERT: D 207 LYS cc_start: 0.7937 (tptp) cc_final: 0.7622 (tmtt) REVERT: D 475 MET cc_start: 0.8219 (mmm) cc_final: 0.7938 (mmt) REVERT: A 621 GLU cc_start: 0.9047 (tt0) cc_final: 0.8409 (tm-30) REVERT: A 625 ASN cc_start: 0.9293 (t0) cc_final: 0.8541 (t0) REVERT: G 16 GLU cc_start: 0.8374 (pm20) cc_final: 0.7979 (pm20) REVERT: G 27 ASP cc_start: 0.9154 (t0) cc_final: 0.8841 (t0) REVERT: G 100 ASP cc_start: 0.8714 (t0) cc_final: 0.8429 (t0) REVERT: J 79 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8053 (mm-30) REVERT: J 82 ASP cc_start: 0.8518 (m-30) cc_final: 0.8250 (m-30) REVERT: F 166 ARG cc_start: 0.4710 (tpt170) cc_final: 0.1118 (tmt170) REVERT: C 621 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8092 (tm-30) REVERT: C 657 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8721 (tm-30) REVERT: I 3 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7839 (mm-40) REVERT: I 5 GLN cc_start: 0.8547 (tp-100) cc_final: 0.8179 (tp40) REVERT: I 27 ASP cc_start: 0.9200 (t70) cc_final: 0.8919 (t0) REVERT: I 72 ASP cc_start: 0.8801 (t70) cc_final: 0.8369 (t0) REVERT: I 100 ASP cc_start: 0.8491 (t70) cc_final: 0.8108 (t70) REVERT: K 17 GLU cc_start: 0.8126 (pm20) cc_final: 0.7914 (pm20) REVERT: K 24 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7929 (tmm160) outliers start: 50 outliers final: 40 residues processed: 264 average time/residue: 0.1631 time to fit residues: 64.8609 Evaluate side-chains 259 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 51 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 107 LEU 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 265 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 145 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 219 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 164 optimal weight: 0.5980 chunk 211 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 652 GLN ** 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 = 0.3193 r_free = 0.3193 target = 0.067592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.050053 restraints weight = 57297.440| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.91 r_work: 0.2687 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20892 Z= 0.119 Angle : 0.615 17.813 28533 Z= 0.294 Chirality : 0.044 0.431 3426 Planarity : 0.003 0.042 3477 Dihedral : 7.164 58.490 4479 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 1.78 % Allowed : 11.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.17), residues: 2394 helix: 2.00 (0.28), residues: 396 sheet: -0.24 (0.18), residues: 810 loop : -0.94 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 617 TYR 0.018 0.001 TYR D 484 PHE 0.011 0.001 PHE D 53 TRP 0.017 0.001 TRP B 571 HIS 0.006 0.001 HIS I 35B Details of bonding type rmsd covalent geometry : bond 0.00270 (20760) covalent geometry : angle 0.56365 (28179) SS BOND : bond 0.00178 ( 42) SS BOND : angle 0.52018 ( 84) hydrogen bonds : bond 0.03563 ( 692) hydrogen bonds : angle 4.80875 ( 1977) link_ALPHA1-3 : bond 0.01161 ( 3) link_ALPHA1-3 : angle 1.46207 ( 9) link_ALPHA1-6 : bond 0.00633 ( 3) link_ALPHA1-6 : angle 1.46866 ( 9) link_BETA1-4 : bond 0.00471 ( 24) link_BETA1-4 : angle 1.35834 ( 72) link_NAG-ASN : bond 0.00553 ( 60) link_NAG-ASN : angle 3.01168 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 0.851 Fit side-chains REVERT: B 621 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8193 (tm-30) REVERT: B 632 ASP cc_start: 0.9314 (t70) cc_final: 0.8889 (t0) REVERT: B 657 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8584 (tm-30) REVERT: H 46 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8193 (mt-10) REVERT: H 72 ASP cc_start: 0.8172 (t70) cc_final: 0.7223 (t0) REVERT: H 75 LYS cc_start: 0.9133 (mtmm) cc_final: 0.8675 (mtmm) REVERT: H 100 ASP cc_start: 0.8662 (t0) cc_final: 0.8277 (t0) REVERT: L 79 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8073 (mm-30) REVERT: L 103 ARG cc_start: 0.7777 (ptm160) cc_final: 0.7377 (ptp-110) REVERT: D 207 LYS cc_start: 0.7886 (tptp) cc_final: 0.7567 (tmtt) REVERT: D 475 MET cc_start: 0.8090 (mmm) cc_final: 0.7636 (mmt) REVERT: A 621 GLU cc_start: 0.8963 (tt0) cc_final: 0.8414 (tm-30) REVERT: A 625 ASN cc_start: 0.9236 (t0) cc_final: 0.8522 (t0) REVERT: A 632 ASP cc_start: 0.9263 (t70) cc_final: 0.8952 (t0) REVERT: G 16 GLU cc_start: 0.8366 (pm20) cc_final: 0.7974 (pm20) REVERT: G 27 ASP cc_start: 0.9116 (t0) cc_final: 0.8502 (t0) REVERT: G 100 ASP cc_start: 0.8632 (t0) cc_final: 0.8239 (t0) REVERT: J 6 GLN cc_start: 0.8514 (mt0) cc_final: 0.8308 (mt0) REVERT: J 79 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8028 (mm-30) REVERT: J 82 ASP cc_start: 0.8497 (m-30) cc_final: 0.8284 (m-30) REVERT: J 100 GLN cc_start: 0.8863 (pm20) cc_final: 0.8506 (pm20) REVERT: F 166 ARG cc_start: 0.4530 (tpt170) cc_final: 0.1133 (tmt170) REVERT: C 621 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8080 (tm-30) REVERT: C 657 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8701 (tm-30) REVERT: C 659 ASP cc_start: 0.8723 (t0) cc_final: 0.8391 (m-30) REVERT: I 3 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7894 (mm-40) REVERT: I 5 GLN cc_start: 0.8533 (tp-100) cc_final: 0.8186 (tp40) REVERT: I 27 ASP cc_start: 0.9194 (t70) cc_final: 0.8901 (t0) REVERT: I 72 ASP cc_start: 0.8790 (t70) cc_final: 0.8357 (t0) REVERT: I 100 ASP cc_start: 0.8341 (t70) cc_final: 0.7907 (t70) REVERT: K 17 GLU cc_start: 0.8032 (pm20) cc_final: 0.7788 (pm20) REVERT: K 24 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8392 (mtp85) outliers start: 38 outliers final: 36 residues processed: 265 average time/residue: 0.1653 time to fit residues: 65.9142 Evaluate side-chains 264 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain 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 Chi-restraints excluded: chain K residue 70 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 190 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3193 r_free = 0.3193 target = 0.067566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.050064 restraints weight = 57441.872| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.91 r_work: 0.2689 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20892 Z= 0.137 Angle : 0.612 17.670 28533 Z= 0.293 Chirality : 0.044 0.414 3426 Planarity : 0.003 0.039 3477 Dihedral : 6.978 56.950 4479 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.59 % Favored : 96.37 % Rotamer: Outliers : 2.15 % Allowed : 11.45 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.17), residues: 2394 helix: 2.05 (0.28), residues: 396 sheet: -0.22 (0.18), residues: 813 loop : -0.89 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 273 TYR 0.019 0.001 TYR D 484 PHE 0.011 0.001 PHE H 78 TRP 0.016 0.001 TRP B 571 HIS 0.005 0.001 HIS I 35B Details of bonding type rmsd covalent geometry : bond 0.00321 (20760) covalent geometry : angle 0.56378 (28179) SS BOND : bond 0.00192 ( 42) SS BOND : angle 0.52656 ( 84) hydrogen bonds : bond 0.03470 ( 692) hydrogen bonds : angle 4.69853 ( 1977) link_ALPHA1-3 : bond 0.01063 ( 3) link_ALPHA1-3 : angle 1.41740 ( 9) link_ALPHA1-6 : bond 0.00545 ( 3) link_ALPHA1-6 : angle 1.49253 ( 9) link_BETA1-4 : bond 0.00493 ( 24) link_BETA1-4 : angle 1.36502 ( 72) link_NAG-ASN : bond 0.00521 ( 60) link_NAG-ASN : angle 2.93125 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 1.107 Fit side-chains REVERT: B 621 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 632 ASP cc_start: 0.9315 (t70) cc_final: 0.8855 (t0) REVERT: B 657 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8564 (tm-30) REVERT: H 46 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8115 (mt-10) REVERT: H 72 ASP cc_start: 0.8190 (t70) cc_final: 0.7258 (t0) REVERT: H 75 LYS cc_start: 0.9139 (mtmm) cc_final: 0.8673 (mtmm) REVERT: H 100 ASP cc_start: 0.8713 (t0) cc_final: 0.8310 (t0) REVERT: L 79 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8179 (mm-30) REVERT: L 103 ARG cc_start: 0.7781 (ptm160) cc_final: 0.7402 (ptp-110) REVERT: D 166 ARG cc_start: 0.4778 (ttt-90) cc_final: 0.4230 (ttt-90) REVERT: D 207 LYS cc_start: 0.7857 (tptp) cc_final: 0.7551 (tmtt) REVERT: A 621 GLU cc_start: 0.8957 (tt0) cc_final: 0.8448 (tm-30) REVERT: A 625 ASN cc_start: 0.9264 (t0) cc_final: 0.8652 (t0) REVERT: A 632 ASP cc_start: 0.9243 (OUTLIER) cc_final: 0.8933 (t0) REVERT: G 16 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7976 (pm20) REVERT: G 27 ASP cc_start: 0.9093 (t0) cc_final: 0.8460 (t0) REVERT: G 100 ASP cc_start: 0.8601 (t0) cc_final: 0.8258 (t0) REVERT: J 6 GLN cc_start: 0.8545 (mt0) cc_final: 0.8284 (mt0) REVERT: J 79 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8084 (mm-30) REVERT: J 82 ASP cc_start: 0.8564 (m-30) cc_final: 0.8342 (m-30) REVERT: J 100 GLN cc_start: 0.8887 (pm20) cc_final: 0.8563 (pm20) REVERT: F 166 ARG cc_start: 0.4484 (tpt170) cc_final: 0.1087 (ttt90) REVERT: C 621 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8119 (tm-30) REVERT: C 657 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8699 (tm-30) REVERT: C 659 ASP cc_start: 0.8751 (t0) cc_final: 0.8408 (m-30) REVERT: I 5 GLN cc_start: 0.8554 (tp-100) cc_final: 0.8199 (tp40) REVERT: I 27 ASP cc_start: 0.9192 (t70) cc_final: 0.8879 (t0) REVERT: I 72 ASP cc_start: 0.8803 (t70) cc_final: 0.8370 (t0) REVERT: I 100 ASP cc_start: 0.8341 (t70) cc_final: 0.7915 (t70) REVERT: K 24 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8389 (mtp85) outliers start: 46 outliers final: 39 residues processed: 269 average time/residue: 0.1687 time to fit residues: 68.7887 Evaluate side-chains 270 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 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 265 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 660 LEU 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 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 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 24 ARG Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 70 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 40 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** J 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 = 0.3187 r_free = 0.3187 target = 0.067282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.049736 restraints weight = 57258.772| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.91 r_work: 0.2680 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20892 Z= 0.160 Angle : 0.631 17.425 28533 Z= 0.302 Chirality : 0.045 0.405 3426 Planarity : 0.003 0.039 3477 Dihedral : 6.972 57.286 4479 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.84 % Favored : 96.12 % Rotamer: Outliers : 2.24 % Allowed : 11.69 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.17), residues: 2394 helix: 2.04 (0.28), residues: 396 sheet: -0.19 (0.18), residues: 810 loop : -0.88 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 273 TYR 0.027 0.001 TYR D 484 PHE 0.012 0.001 PHE H 78 TRP 0.018 0.001 TRP C 571 HIS 0.005 0.001 HIS I 35B Details of bonding type rmsd covalent geometry : bond 0.00379 (20760) covalent geometry : angle 0.58420 (28179) SS BOND : bond 0.00211 ( 42) SS BOND : angle 0.58335 ( 84) hydrogen bonds : bond 0.03545 ( 692) hydrogen bonds : angle 4.68194 ( 1977) link_ALPHA1-3 : bond 0.00967 ( 3) link_ALPHA1-3 : angle 1.33333 ( 9) link_ALPHA1-6 : bond 0.00460 ( 3) link_ALPHA1-6 : angle 1.50714 ( 9) link_BETA1-4 : bond 0.00491 ( 24) link_BETA1-4 : angle 1.36501 ( 72) link_NAG-ASN : bond 0.00529 ( 60) link_NAG-ASN : angle 2.91936 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8240 (tm-30) REVERT: B 632 ASP cc_start: 0.9328 (t70) cc_final: 0.8869 (t0) REVERT: H 46 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8146 (mt-10) REVERT: H 100 ASP cc_start: 0.8717 (t0) cc_final: 0.8325 (t0) REVERT: L 79 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8035 (mm-30) REVERT: L 103 ARG cc_start: 0.7766 (ptm160) cc_final: 0.7394 (ptp-110) REVERT: D 166 ARG cc_start: 0.4769 (ttt-90) cc_final: 0.3680 (ttt90) REVERT: D 207 LYS cc_start: 0.7892 (tptp) cc_final: 0.7598 (tmtt) REVERT: A 621 GLU cc_start: 0.8972 (tt0) cc_final: 0.8453 (tm-30) REVERT: A 625 ASN cc_start: 0.9268 (t0) cc_final: 0.8615 (t0) REVERT: A 632 ASP cc_start: 0.9256 (t70) cc_final: 0.8952 (t0) REVERT: G 16 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: G 27 ASP cc_start: 0.9118 (t0) cc_final: 0.8497 (t0) REVERT: G 100 ASP cc_start: 0.8608 (t0) cc_final: 0.8257 (t0) REVERT: G 105 GLN cc_start: 0.9105 (pt0) cc_final: 0.8656 (pm20) REVERT: J 6 GLN cc_start: 0.8589 (mt0) cc_final: 0.8274 (mt0) REVERT: J 79 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8096 (mm-30) REVERT: J 100 GLN cc_start: 0.8898 (pm20) cc_final: 0.8564 (pm20) REVERT: F 166 ARG cc_start: 0.4515 (tpt170) cc_final: 0.1087 (ttt90) REVERT: C 621 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8119 (tm-30) REVERT: C 657 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8698 (tm-30) REVERT: C 659 ASP cc_start: 0.8782 (t0) cc_final: 0.8416 (m-30) REVERT: I 27 ASP cc_start: 0.9196 (t70) cc_final: 0.8882 (t0) REVERT: I 72 ASP cc_start: 0.8805 (t70) cc_final: 0.8367 (t0) REVERT: I 100 ASP cc_start: 0.8385 (t70) cc_final: 0.7956 (t70) REVERT: K 24 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8385 (mtp85) outliers start: 48 outliers final: 43 residues processed: 266 average time/residue: 0.1680 time to fit residues: 67.6106 Evaluate side-chains 272 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 227 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 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 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 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 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 I residue 89 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 167 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 162 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN K 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.066822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.049530 restraints weight = 57998.646| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.88 r_work: 0.2657 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3574 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= 0.205 Angle : 0.662 16.875 28533 Z= 0.320 Chirality : 0.046 0.392 3426 Planarity : 0.003 0.044 3477 Dihedral : 7.106 59.170 4479 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.86 % Rotamer: Outliers : 2.29 % Allowed : 11.87 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.17), residues: 2394 helix: 1.96 (0.28), residues: 396 sheet: -0.23 (0.18), residues: 813 loop : -0.91 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 273 TYR 0.026 0.001 TYR D 484 PHE 0.016 0.001 PHE H 78 TRP 0.017 0.001 TRP B 571 HIS 0.005 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00489 (20760) covalent geometry : angle 0.61698 (28179) SS BOND : bond 0.00252 ( 42) SS BOND : angle 0.68025 ( 84) hydrogen bonds : bond 0.03864 ( 692) hydrogen bonds : angle 4.77669 ( 1977) link_ALPHA1-3 : bond 0.00862 ( 3) link_ALPHA1-3 : angle 1.34728 ( 9) link_ALPHA1-6 : bond 0.00348 ( 3) link_ALPHA1-6 : angle 1.57700 ( 9) link_BETA1-4 : bond 0.00482 ( 24) link_BETA1-4 : angle 1.40738 ( 72) link_NAG-ASN : bond 0.00548 ( 60) link_NAG-ASN : angle 2.95696 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 227 time to evaluate : 0.883 Fit side-chains REVERT: B 621 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8267 (tm-30) REVERT: B 632 ASP cc_start: 0.9358 (t70) cc_final: 0.8928 (t0) REVERT: H 46 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8164 (mt-10) REVERT: H 75 LYS cc_start: 0.9280 (mtmm) cc_final: 0.9066 (mtmm) REVERT: H 100 ASP cc_start: 0.8768 (t0) cc_final: 0.8368 (t0) REVERT: L 60 ASP cc_start: 0.8581 (p0) cc_final: 0.8368 (p0) REVERT: L 79 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8229 (mm-30) REVERT: L 103 ARG cc_start: 0.7779 (ptm160) cc_final: 0.7398 (ptp-110) REVERT: D 166 ARG cc_start: 0.4807 (ttt-90) cc_final: 0.3714 (ttt90) REVERT: D 207 LYS cc_start: 0.7931 (tptp) cc_final: 0.7640 (tmtt) REVERT: A 625 ASN cc_start: 0.9248 (t0) cc_final: 0.8582 (t0) REVERT: A 632 ASP cc_start: 0.9288 (t70) cc_final: 0.8991 (t0) REVERT: G 16 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7976 (pm20) REVERT: G 27 ASP cc_start: 0.9163 (t0) cc_final: 0.8816 (t0) REVERT: G 100 ASP cc_start: 0.8647 (t0) cc_final: 0.8398 (t0) REVERT: J 79 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8132 (mm-30) REVERT: J 82 ASP cc_start: 0.8399 (m-30) cc_final: 0.8177 (m-30) REVERT: F 166 ARG cc_start: 0.4582 (tpt170) cc_final: 0.1035 (tmt170) REVERT: C 621 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8294 (tm-30) REVERT: C 657 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8717 (tm-30) REVERT: C 659 ASP cc_start: 0.8834 (t0) cc_final: 0.8476 (m-30) REVERT: I 27 ASP cc_start: 0.9183 (t70) cc_final: 0.8872 (t0) REVERT: I 72 ASP cc_start: 0.8832 (t70) cc_final: 0.8399 (t0) REVERT: I 100 ASP cc_start: 0.8488 (t70) cc_final: 0.8060 (t70) REVERT: K 24 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8407 (mtp85) REVERT: K 100 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8822 (pm20) outliers start: 49 outliers final: 44 residues processed: 262 average time/residue: 0.1713 time to fit residues: 67.5959 Evaluate side-chains 267 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 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 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 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 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 5 GLN 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 24 ARG Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 100 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 217 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 15 optimal weight: 0.0070 chunk 88 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 616 ASN K 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.071811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.053290 restraints weight = 59183.924| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.95 r_work: 0.2701 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20892 Z= 0.106 Angle : 0.620 18.060 28533 Z= 0.297 Chirality : 0.044 0.388 3426 Planarity : 0.003 0.037 3477 Dihedral : 6.818 56.760 4479 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.70 % Rotamer: Outliers : 2.20 % Allowed : 12.44 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.17), residues: 2394 helix: 2.03 (0.28), residues: 396 sheet: -0.11 (0.18), residues: 810 loop : -0.89 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 273 TYR 0.026 0.001 TYR D 484 PHE 0.010 0.001 PHE I 91 TRP 0.021 0.001 TRP B 571 HIS 0.006 0.001 HIS I 35B Details of bonding type rmsd covalent geometry : bond 0.00239 (20760) covalent geometry : angle 0.57396 (28179) SS BOND : bond 0.00169 ( 42) SS BOND : angle 0.50950 ( 84) hydrogen bonds : bond 0.03245 ( 692) hydrogen bonds : angle 4.60817 ( 1977) link_ALPHA1-3 : bond 0.00901 ( 3) link_ALPHA1-3 : angle 1.19554 ( 9) link_ALPHA1-6 : bond 0.00503 ( 3) link_ALPHA1-6 : angle 1.46367 ( 9) link_BETA1-4 : bond 0.00495 ( 24) link_BETA1-4 : angle 1.25521 ( 72) link_NAG-ASN : bond 0.00526 ( 60) link_NAG-ASN : angle 2.90204 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6952.25 seconds wall clock time: 119 minutes 43.02 seconds (7183.02 seconds total)