Starting phenix.real_space_refine on Tue Jun 17 23:39:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8to7_41438/06_2025/8to7_41438.cif Found real_map, /net/cci-nas-00/data/ceres_data/8to7_41438/06_2025/8to7_41438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8to7_41438/06_2025/8to7_41438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8to7_41438/06_2025/8to7_41438.map" model { file = "/net/cci-nas-00/data/ceres_data/8to7_41438/06_2025/8to7_41438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8to7_41438/06_2025/8to7_41438.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 12738 2.51 5 N 3423 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20361 Number of models: 1 Model: "" Number of chains: 33 Chain: "E" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "H" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "A" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "G" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "J" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "C" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "K" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 24.47, per 1000 atoms: 1.20 Number of scatterers: 20361 At special positions: 0 Unit cell: (132.72, 139.02, 136.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4080 8.00 N 3423 7.00 C 12738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 433 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.04 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS A 605 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " " BMA U 3 " - " MAN U 5 " " BMA Z 3 " - " MAN Z 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG A 701 " - " ASN A 618 " " NAG A 702 " - " ASN A 611 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 611 " " NAG C 701 " - " ASN C 618 " " NAG C 702 " - " ASN C 611 " " NAG D 601 " - " ASN D 133 " " NAG D 602 " - " ASN D 197 " " NAG D 603 " - " ASN D 234 " " NAG D 604 " - " ASN D 276 " " NAG D 605 " - " ASN D 295 " " NAG D 606 " - " ASN D 301 " " NAG D 607 " - " ASN D 332 " " NAG D 608 " - " ASN D 339 " " NAG D 609 " - " ASN D 355 " " NAG D 610 " - " ASN D 363 " " NAG D 611 " - " ASN D 386 " " NAG D 612 " - " ASN D 392 " " NAG D 613 " - " ASN D 448 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 197 " " NAG E 603 " - " ASN E 234 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 295 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 332 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 355 " " NAG E 610 " - " ASN E 363 " " NAG E 611 " - " ASN E 386 " " NAG E 612 " - " ASN E 392 " " NAG E 613 " - " ASN E 448 " " NAG F 601 " - " ASN F 133 " " NAG F 602 " - " ASN F 197 " " NAG F 603 " - " ASN F 234 " " NAG F 604 " - " ASN F 276 " " NAG F 605 " - " ASN F 295 " " NAG F 606 " - " ASN F 301 " " NAG F 607 " - " ASN F 332 " " NAG F 608 " - " ASN F 339 " " NAG F 609 " - " ASN F 355 " " NAG F 610 " - " ASN F 363 " " NAG F 611 " - " ASN F 386 " " NAG F 612 " - " ASN F 392 " " NAG F 613 " - " ASN F 448 " " NAG M 1 " - " ASN E 88 " " NAG N 1 " - " ASN E 156 " " NAG O 1 " - " ASN E 160 " " NAG P 1 " - " ASN E 262 " " NAG Q 1 " - " ASN B 637 " " NAG R 1 " - " ASN D 88 " " NAG S 1 " - " ASN D 156 " " NAG T 1 " - " ASN D 160 " " NAG U 1 " - " ASN D 262 " " NAG V 1 " - " ASN A 637 " " NAG W 1 " - " ASN F 88 " " NAG X 1 " - " ASN F 156 " " NAG Y 1 " - " ASN F 160 " " NAG Z 1 " - " ASN F 262 " " NAG a 1 " - " ASN C 637 " Time building additional restraints: 5.60 Conformation dependent library (CDL) restraints added in 2.6 seconds 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4506 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 42 sheets defined 19.3% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'E' and resid 98 through 115 removed outlier: 4.452A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.743A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 126' Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.057A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.573A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.918A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.529A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 626 removed outlier: 3.570A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.638A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.151A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 116 removed outlier: 4.525A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.566A pdb=" N LEU D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS D 126 " --> pdb=" O THR D 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 126' Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 351 removed outlier: 4.293A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 475 through 481 removed outlier: 3.515A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 4.090A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 596 removed outlier: 3.505A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 615 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 662 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'F' and resid 98 through 115 removed outlier: 4.481A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.885A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.512A pdb=" N THR F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 390 Processing helix chain 'F' and resid 475 through 481 removed outlier: 3.724A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 527 removed outlier: 4.278A pdb=" N GLY C 527 " --> pdb=" O GLY C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 542 removed outlier: 4.168A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 596 removed outlier: 3.619A pdb=" N TRP C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 615 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 636 Processing helix chain 'C' and resid 638 through 664 removed outlier: 3.914A pdb=" N LEU C 663 " --> pdb=" O ASP C 659 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.470A pdb=" N VAL B 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL E 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR B 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N TYR E 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N CYS B 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.082A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.502A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE E 53 " --> pdb=" O CYS E 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.946A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.785A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.938A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.223A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.300A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.430A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.898A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.189A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 359 through 361 Processing sheet with id=AA7, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.189A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.898A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.430A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.300A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.223A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 413 through 420 removed outlier: 3.725A pdb=" N PHE E 383 " --> pdb=" O PHE E 376 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.571A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.511A pdb=" N PHE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.531A pdb=" N LEU H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR H 35 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP H 35A" --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ARG H 38 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLY H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.252A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.252A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AB6, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.582A pdb=" N LYS D 487 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 75 through 76 removed outlier: 3.527A pdb=" N PHE D 53 " --> pdb=" O CYS D 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.689A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 169 through 177 removed outlier: 3.757A pdb=" N LYS D 189 " --> pdb=" O CYS D 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.586A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 271 through 273 removed outlier: 3.670A pdb=" N ILE D 443 " --> pdb=" O ARG D 298 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS D 330 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU D 381 " --> pdb=" O CYS D 378 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.603A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.564A pdb=" N GLN G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AC6, first strand: chain 'G' and resid 57 through 59 removed outlier: 3.575A pdb=" N GLY G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL G 89 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 57 through 59 removed outlier: 3.575A pdb=" N GLY G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP G 35A" --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL G 89 " --> pdb=" O GLN G 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.542A pdb=" N ALA J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP J 70 " --> pdb=" O ALA J 67 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.952A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU J 33 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.952A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 494 through 499 removed outlier: 6.174A pdb=" N VAL C 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N VAL F 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR C 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N TYR F 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N CYS C 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.181A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.713A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER F 56 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE F 53 " --> pdb=" O CYS F 218 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 91 through 93 removed outlier: 3.566A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY F 237 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 169 through 177 removed outlier: 3.583A pdb=" N LYS F 189 " --> pdb=" O CYS F 131 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.357A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 259 through 261 removed outlier: 3.736A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE F 376 " --> pdb=" O PHE F 383 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 271 through 273 removed outlier: 3.562A pdb=" N MET F 271 " --> pdb=" O GLN F 287 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE F 359 " --> pdb=" O TRP F 395 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 304 through 312 removed outlier: 3.565A pdb=" N ILE F 309 " --> pdb=" O GLN F 315 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.592A pdb=" N ALA I 88 " --> pdb=" O VAL I 109 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TRP I 35A" --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYR I 50 " --> pdb=" O TRP I 35A" (cutoff:3.500A) removed outlier: 7.287A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY I 44 " --> pdb=" O SER I 40 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.592A pdb=" N ALA I 88 " --> pdb=" O VAL I 109 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG I 96 " --> pdb=" O VAL I 100G" (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL I 100G" --> pdb=" O ARG I 96 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.635A pdb=" N ALA K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.892A pdb=" N ASP K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL K 104 " --> pdb=" O GLY K 84 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU K 33 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 1977 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.59 Time building geometry restraints manager: 6.58 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: 936.470 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: 0.040 Extract box with map and model: 1.450 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 61.360 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 1003.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20892 Z= 0.334 Angle : 1.123 16.234 28533 Z= 0.583 Chirality : 0.069 0.927 3426 Planarity : 0.006 0.265 3477 Dihedral : 15.433 108.794 8973 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2394 helix: 1.43 (0.28), residues: 393 sheet: -1.01 (0.19), residues: 699 loop : -0.99 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 427 HIS 0.025 0.002 HIS I 35B PHE 0.018 0.002 PHE E 233 TYR 0.034 0.002 TYR D 486 ARG 0.011 0.001 ARG D 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 60) link_NAG-ASN : angle 3.13279 ( 180) link_ALPHA1-6 : bond 0.00231 ( 3) link_ALPHA1-6 : angle 1.52907 ( 9) link_BETA1-4 : bond 0.00928 ( 24) link_BETA1-4 : angle 2.38653 ( 72) link_ALPHA1-3 : bond 0.00570 ( 3) link_ALPHA1-3 : angle 1.20891 ( 9) hydrogen bonds : bond 0.23818 ( 692) hydrogen bonds : angle 8.29025 ( 1977) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.30042 ( 84) covalent geometry : bond 0.00628 (20760) covalent geometry : angle 1.09252 (28179) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 2.110 Fit side-chains revert: symmetry clash REVERT: E 161 MET cc_start: 0.8325 (tpt) cc_final: 0.7947 (tpt) REVERT: E 166 ARG cc_start: 0.4309 (ttt-90) cc_final: 0.3242 (ttt-90) REVERT: E 462 ASN cc_start: 0.7978 (t0) cc_final: 0.7764 (t0) REVERT: E 475 MET cc_start: 0.8805 (mmm) cc_final: 0.8253 (mmp) REVERT: B 625 ASN cc_start: 0.9150 (t0) cc_final: 0.8798 (t0) REVERT: H 46 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7870 (mt-10) REVERT: H 72 ASP cc_start: 0.8409 (t70) cc_final: 0.7541 (t0) REVERT: L 103 ARG cc_start: 0.8030 (ptm160) cc_final: 0.7389 (ptp-110) REVERT: D 475 MET cc_start: 0.8112 (mmm) cc_final: 0.7867 (mmt) REVERT: A 625 ASN cc_start: 0.9038 (t0) cc_final: 0.8606 (t0) REVERT: G 75 LYS cc_start: 0.8336 (ptpp) cc_final: 0.7724 (ptpp) REVERT: G 100 ASP cc_start: 0.8078 (t0) cc_final: 0.7621 (t0) REVERT: G 105 GLN cc_start: 0.8914 (pt0) cc_final: 0.8058 (pt0) REVERT: G 107 LEU cc_start: 0.8324 (tp) cc_final: 0.7964 (tp) REVERT: G 110 THR cc_start: 0.8671 (m) cc_final: 0.8408 (p) REVERT: F 166 ARG cc_start: 0.4144 (tpt170) cc_final: 0.1499 (tmt170) REVERT: F 293 GLN cc_start: 0.8535 (mt0) cc_final: 0.8335 (mt0) REVERT: F 479 TRP cc_start: 0.8357 (m-10) cc_final: 0.8141 (m-10) REVERT: I 27 ASP cc_start: 0.9190 (t70) cc_final: 0.8948 (t0) REVERT: I 72 ASP cc_start: 0.8739 (t70) cc_final: 0.8332 (t0) REVERT: I 95 GLU cc_start: 0.8059 (pt0) cc_final: 0.7757 (pt0) REVERT: I 100 ILE cc_start: 0.8715 (mm) cc_final: 0.8295 (mm) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.3423 time to fit residues: 156.7373 Evaluate side-chains 237 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN ** J 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN F 352 HIS C 653 GLN K 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.069293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.050801 restraints weight = 58555.319| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 4.15 r_work: 0.2607 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 20892 Z= 0.269 Angle : 0.738 12.207 28533 Z= 0.363 Chirality : 0.050 0.501 3426 Planarity : 0.004 0.055 3477 Dihedral : 10.848 77.569 4479 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.45 % Allowed : 6.31 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2394 helix: 1.56 (0.28), residues: 408 sheet: -0.58 (0.18), residues: 753 loop : -0.96 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 571 HIS 0.008 0.001 HIS F 105 PHE 0.017 0.002 PHE D 383 TYR 0.016 0.002 TYR B 638 ARG 0.006 0.001 ARG C 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 60) link_NAG-ASN : angle 2.74241 ( 180) link_ALPHA1-6 : bond 0.00134 ( 3) link_ALPHA1-6 : angle 2.05380 ( 9) link_BETA1-4 : bond 0.00717 ( 24) link_BETA1-4 : angle 2.29856 ( 72) link_ALPHA1-3 : bond 0.00829 ( 3) link_ALPHA1-3 : angle 2.84956 ( 9) hydrogen bonds : bond 0.04673 ( 692) hydrogen bonds : angle 5.85737 ( 1977) SS BOND : bond 0.00356 ( 42) SS BOND : angle 0.97894 ( 84) covalent geometry : bond 0.00638 (20760) covalent geometry : angle 0.69494 (28179) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 245 time to evaluate : 2.291 Fit side-chains REVERT: E 161 MET cc_start: 0.8791 (tpt) cc_final: 0.8420 (tpt) REVERT: E 377 ASN cc_start: 0.9239 (p0) cc_final: 0.9030 (p0) REVERT: E 475 MET cc_start: 0.8969 (mmm) cc_final: 0.8636 (tpp) REVERT: B 621 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7918 (tm-30) REVERT: B 625 ASN cc_start: 0.9025 (t0) cc_final: 0.8556 (t0) REVERT: B 632 ASP cc_start: 0.9131 (t0) cc_final: 0.8798 (t0) REVERT: H 16 GLU cc_start: 0.8655 (pm20) cc_final: 0.8410 (pm20) REVERT: H 46 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8279 (mt-10) REVERT: H 72 ASP cc_start: 0.7979 (t70) cc_final: 0.7339 (t0) REVERT: H 75 LYS cc_start: 0.8978 (mtmm) cc_final: 0.8694 (mtmm) REVERT: H 100 TYR cc_start: 0.8697 (m-80) cc_final: 0.8290 (m-80) REVERT: H 100 ASP cc_start: 0.8499 (t0) cc_final: 0.8226 (t0) REVERT: L 79 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7420 (mm-30) REVERT: L 103 ARG cc_start: 0.7553 (ptm160) cc_final: 0.7077 (ptp-110) REVERT: D 166 ARG cc_start: 0.4784 (ttt-90) cc_final: 0.4351 (ttt-90) REVERT: A 621 GLU cc_start: 0.8962 (tt0) cc_final: 0.8114 (tm-30) REVERT: A 625 ASN cc_start: 0.9219 (t0) cc_final: 0.8629 (t0) REVERT: G 3 GLN cc_start: 0.8464 (mm110) cc_final: 0.8248 (mm110) REVERT: G 5 GLN cc_start: 0.8539 (tp-100) cc_final: 0.8303 (tp-100) REVERT: G 16 GLU cc_start: 0.8222 (pm20) cc_final: 0.7651 (pm20) REVERT: G 72 ASP cc_start: 0.8050 (p0) cc_final: 0.7619 (p0) REVERT: G 100 ASP cc_start: 0.8706 (t0) cc_final: 0.8331 (t0) REVERT: G 105 GLN cc_start: 0.8970 (pt0) cc_final: 0.8637 (pt0) REVERT: G 111 VAL cc_start: 0.9325 (t) cc_final: 0.9048 (m) REVERT: J 17 GLU cc_start: 0.7173 (pm20) cc_final: 0.6952 (pm20) REVERT: J 79 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7628 (mm-30) REVERT: J 82 ASP cc_start: 0.8084 (m-30) cc_final: 0.7576 (m-30) REVERT: F 166 ARG cc_start: 0.4524 (tpt170) cc_final: 0.1204 (tmt170) REVERT: F 475 MET cc_start: 0.8817 (tpp) cc_final: 0.8577 (tpp) REVERT: C 621 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7900 (tm-30) REVERT: I 5 GLN cc_start: 0.8529 (tp-100) cc_final: 0.8094 (tp40) REVERT: I 27 ASP cc_start: 0.9274 (t70) cc_final: 0.8846 (t70) REVERT: I 72 ASP cc_start: 0.8712 (t70) cc_final: 0.8401 (t0) REVERT: I 100 ILE cc_start: 0.8993 (mm) cc_final: 0.8567 (mm) REVERT: I 100 ASP cc_start: 0.8472 (t0) cc_final: 0.8223 (t70) REVERT: K 24 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7607 (tmm160) REVERT: K 81 GLU cc_start: 0.8214 (pm20) cc_final: 0.8011 (pm20) outliers start: 31 outliers final: 25 residues processed: 262 average time/residue: 0.3523 time to fit residues: 139.1649 Evaluate side-chains 244 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 83 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 28 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 117 optimal weight: 0.0670 chunk 11 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 200 optimal weight: 0.0370 overall best weight: 1.2202 ------------------------------------------------------------------------------- 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** ** J 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.069577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.051681 restraints weight = 56419.146| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 3.90 r_work: 0.2640 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2158 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= 0.126 Angle : 0.623 12.358 28533 Z= 0.298 Chirality : 0.046 0.471 3426 Planarity : 0.003 0.048 3477 Dihedral : 8.884 68.030 4479 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.40 % Allowed : 7.95 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.17), residues: 2394 helix: 1.73 (0.28), residues: 405 sheet: -0.51 (0.18), residues: 786 loop : -0.86 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 479 HIS 0.009 0.001 HIS I 35B PHE 0.011 0.001 PHE J 87 TYR 0.012 0.001 TYR F 173 ARG 0.005 0.000 ARG C 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 60) link_NAG-ASN : angle 2.82074 ( 180) link_ALPHA1-6 : bond 0.00539 ( 3) link_ALPHA1-6 : angle 1.87308 ( 9) link_BETA1-4 : bond 0.00564 ( 24) link_BETA1-4 : angle 1.87972 ( 72) link_ALPHA1-3 : bond 0.01117 ( 3) link_ALPHA1-3 : angle 1.75162 ( 9) hydrogen bonds : bond 0.03982 ( 692) hydrogen bonds : angle 5.32520 ( 1977) SS BOND : bond 0.00206 ( 42) SS BOND : angle 0.53068 ( 84) covalent geometry : bond 0.00289 (20760) covalent geometry : angle 0.57434 (28179) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 2.117 Fit side-chains REVERT: E 475 MET cc_start: 0.8891 (mmm) cc_final: 0.8440 (tpp) REVERT: B 613 SER cc_start: 0.9517 (m) cc_final: 0.9292 (t) REVERT: B 621 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7836 (tm-30) REVERT: B 625 ASN cc_start: 0.9045 (t0) cc_final: 0.8459 (t0) REVERT: B 632 ASP cc_start: 0.9119 (t70) cc_final: 0.8731 (t0) REVERT: H 27 ASP cc_start: 0.9203 (t0) cc_final: 0.8977 (t0) REVERT: H 46 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8109 (mt-10) REVERT: H 72 ASP cc_start: 0.7922 (t70) cc_final: 0.7126 (t0) REVERT: H 75 LYS cc_start: 0.9023 (mtmm) cc_final: 0.8551 (mtmm) REVERT: H 100 TYR cc_start: 0.8859 (m-80) cc_final: 0.8435 (m-80) REVERT: H 100 ASP cc_start: 0.8499 (t0) cc_final: 0.8088 (t0) REVERT: L 79 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7554 (mm-30) REVERT: L 103 ARG cc_start: 0.7535 (ptm160) cc_final: 0.7074 (ptp-110) REVERT: D 166 ARG cc_start: 0.4730 (ttt-90) cc_final: 0.4380 (ttt-90) REVERT: A 621 GLU cc_start: 0.8936 (tt0) cc_final: 0.8166 (tm-30) REVERT: A 625 ASN cc_start: 0.9204 (t0) cc_final: 0.8570 (t0) REVERT: G 3 GLN cc_start: 0.8446 (mm110) cc_final: 0.8231 (mm110) REVERT: G 5 GLN cc_start: 0.8591 (tp-100) cc_final: 0.8370 (tp-100) REVERT: G 16 GLU cc_start: 0.8329 (pm20) cc_final: 0.8060 (pm20) REVERT: G 27 ASP cc_start: 0.8890 (t0) cc_final: 0.8380 (t0) REVERT: G 100 ASP cc_start: 0.8591 (t0) cc_final: 0.8171 (t0) REVERT: G 105 GLN cc_start: 0.9052 (pt0) cc_final: 0.8736 (pt0) REVERT: J 6 GLN cc_start: 0.8321 (mt0) cc_final: 0.7981 (mt0) REVERT: J 17 GLU cc_start: 0.7207 (pm20) cc_final: 0.6958 (pm20) REVERT: J 79 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7624 (mm-30) REVERT: J 82 ASP cc_start: 0.8096 (m-30) cc_final: 0.7728 (m-30) REVERT: J 100 GLN cc_start: 0.8941 (pm20) cc_final: 0.8539 (pm20) REVERT: F 166 ARG cc_start: 0.4394 (tpt170) cc_final: 0.0828 (tmt170) REVERT: C 632 ASP cc_start: 0.8961 (t70) cc_final: 0.8691 (t0) REVERT: C 657 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8526 (tm-30) REVERT: C 659 ASP cc_start: 0.8659 (t0) cc_final: 0.8224 (m-30) REVERT: I 3 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7708 (mp10) REVERT: I 5 GLN cc_start: 0.8479 (tp-100) cc_final: 0.8076 (tp40) REVERT: I 16 GLU cc_start: 0.8296 (pm20) cc_final: 0.7965 (pm20) REVERT: I 27 ASP cc_start: 0.9287 (t70) cc_final: 0.8958 (t0) REVERT: I 72 ASP cc_start: 0.8652 (t70) cc_final: 0.8249 (t0) REVERT: I 100 ILE cc_start: 0.9050 (mm) cc_final: 0.8640 (mm) REVERT: I 100 ASP cc_start: 0.8318 (t0) cc_final: 0.8000 (t70) REVERT: K 24 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7659 (tmm160) outliers start: 30 outliers final: 23 residues processed: 269 average time/residue: 0.3274 time to fit residues: 133.3971 Evaluate side-chains 251 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 2.372 ------------------------------------------------------------------------------- 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 H residue 80 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 83 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 208 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 214 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 100 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 GLN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.066156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.047947 restraints weight = 57837.455| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.91 r_work: 0.2538 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 20892 Z= 0.251 Angle : 0.707 16.658 28533 Z= 0.344 Chirality : 0.048 0.480 3426 Planarity : 0.004 0.053 3477 Dihedral : 7.927 59.535 4479 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.86 % Rotamer: Outliers : 2.43 % Allowed : 8.42 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2394 helix: 1.65 (0.28), residues: 405 sheet: -0.52 (0.18), residues: 813 loop : -1.00 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 479 HIS 0.007 0.001 HIS I 35B PHE 0.016 0.002 PHE D 53 TYR 0.015 0.001 TYR D 484 ARG 0.006 0.001 ARG C 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00718 ( 60) link_NAG-ASN : angle 3.02603 ( 180) link_ALPHA1-6 : bond 0.00682 ( 3) link_ALPHA1-6 : angle 2.15931 ( 9) link_BETA1-4 : bond 0.00471 ( 24) link_BETA1-4 : angle 1.83723 ( 72) link_ALPHA1-3 : bond 0.00942 ( 3) link_ALPHA1-3 : angle 2.04075 ( 9) hydrogen bonds : bond 0.04436 ( 692) hydrogen bonds : angle 5.18642 ( 1977) SS BOND : bond 0.00300 ( 42) SS BOND : angle 0.85646 ( 84) covalent geometry : bond 0.00599 (20760) covalent geometry : angle 0.65897 (28179) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 224 time to evaluate : 2.170 Fit side-chains REVERT: E 475 MET cc_start: 0.8830 (mmm) cc_final: 0.8431 (tpp) REVERT: B 621 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7811 (tm-30) REVERT: B 625 ASN cc_start: 0.8983 (t0) cc_final: 0.8675 (m-40) REVERT: B 632 ASP cc_start: 0.9164 (t70) cc_final: 0.8761 (t0) REVERT: H 31 ARG cc_start: 0.8770 (tpt-90) cc_final: 0.8548 (tpt-90) REVERT: H 46 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8189 (mt-10) REVERT: H 72 ASP cc_start: 0.7869 (t70) cc_final: 0.7090 (t0) REVERT: H 75 LYS cc_start: 0.9001 (mtmm) cc_final: 0.8624 (mtmm) REVERT: H 100 ASP cc_start: 0.8708 (t0) cc_final: 0.8233 (t0) REVERT: L 103 ARG cc_start: 0.7517 (ptm160) cc_final: 0.7073 (ptp-110) REVERT: D 166 ARG cc_start: 0.4604 (ttt-90) cc_final: 0.4344 (ttt-90) REVERT: A 621 GLU cc_start: 0.9023 (tt0) cc_final: 0.8212 (tm-30) REVERT: A 625 ASN cc_start: 0.9324 (t0) cc_final: 0.8615 (t0) REVERT: G 5 GLN cc_start: 0.8563 (tp-100) cc_final: 0.8353 (tp-100) REVERT: G 16 GLU cc_start: 0.8331 (pm20) cc_final: 0.7713 (pm20) REVERT: G 27 ASP cc_start: 0.8985 (t0) cc_final: 0.8759 (t0) REVERT: G 100 ASP cc_start: 0.8788 (t0) cc_final: 0.8457 (t0) REVERT: G 105 GLN cc_start: 0.9061 (pt0) cc_final: 0.8749 (pt0) REVERT: J 79 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7847 (mm-30) REVERT: J 100 GLN cc_start: 0.8885 (pm20) cc_final: 0.8671 (pm20) REVERT: F 166 ARG cc_start: 0.4471 (tpt170) cc_final: 0.1151 (tmt170) REVERT: C 621 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7934 (tm-30) REVERT: C 657 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8546 (tm-30) REVERT: I 5 GLN cc_start: 0.8493 (tp-100) cc_final: 0.8131 (tp40) REVERT: I 27 ASP cc_start: 0.9282 (t70) cc_final: 0.8944 (t0) REVERT: I 72 ASP cc_start: 0.8635 (t70) cc_final: 0.8206 (t0) REVERT: I 100 ILE cc_start: 0.9190 (mm) cc_final: 0.8947 (mm) REVERT: K 24 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7790 (tmm160) outliers start: 52 outliers final: 37 residues processed: 261 average time/residue: 0.3378 time to fit residues: 132.4671 Evaluate side-chains 250 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 2.160 ------------------------------------------------------------------------------- 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 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain 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 56 ILE Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 62 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3127 r_free = 0.3127 target = 0.066777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.047992 restraints weight = 59151.471| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 4.16 r_work: 0.2539 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20892 Z= 0.201 Angle : 0.655 16.038 28533 Z= 0.315 Chirality : 0.046 0.463 3426 Planarity : 0.004 0.043 3477 Dihedral : 7.742 59.913 4479 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.59 % Favored : 96.37 % Rotamer: Outliers : 2.24 % Allowed : 10.00 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2394 helix: 1.73 (0.28), residues: 405 sheet: -0.49 (0.18), residues: 819 loop : -1.01 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 571 HIS 0.007 0.001 HIS I 35B PHE 0.014 0.001 PHE D 53 TYR 0.013 0.001 TYR F 173 ARG 0.007 0.000 ARG F 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00568 ( 60) link_NAG-ASN : angle 3.07511 ( 180) link_ALPHA1-6 : bond 0.00556 ( 3) link_ALPHA1-6 : angle 1.57792 ( 9) link_BETA1-4 : bond 0.00499 ( 24) link_BETA1-4 : angle 1.49623 ( 72) link_ALPHA1-3 : bond 0.01086 ( 3) link_ALPHA1-3 : angle 1.72342 ( 9) hydrogen bonds : bond 0.03990 ( 692) hydrogen bonds : angle 5.00332 ( 1977) SS BOND : bond 0.00285 ( 42) SS BOND : angle 0.67559 ( 84) covalent geometry : bond 0.00477 (20760) covalent geometry : angle 0.60415 (28179) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 2.394 Fit side-chains revert: symmetry clash REVERT: E 475 MET cc_start: 0.8943 (mmm) cc_final: 0.7753 (mmm) REVERT: B 621 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8116 (tm-30) REVERT: B 625 ASN cc_start: 0.9028 (t0) cc_final: 0.8718 (m-40) REVERT: B 632 ASP cc_start: 0.9210 (t70) cc_final: 0.8807 (t0) REVERT: B 657 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8490 (tm-30) REVERT: H 31 ARG cc_start: 0.8789 (tpt-90) cc_final: 0.8581 (tpt-90) REVERT: H 46 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8091 (mt-10) REVERT: H 72 ASP cc_start: 0.7938 (t70) cc_final: 0.7068 (t0) REVERT: H 75 LYS cc_start: 0.9048 (mtmm) cc_final: 0.8626 (mtmm) REVERT: H 100 ASP cc_start: 0.8755 (t0) cc_final: 0.8373 (t0) REVERT: L 103 ARG cc_start: 0.7573 (ptm160) cc_final: 0.7167 (ptp-110) REVERT: D 166 ARG cc_start: 0.4645 (ttt-90) cc_final: 0.4425 (ttt-90) REVERT: A 621 GLU cc_start: 0.8994 (tt0) cc_final: 0.8219 (tm-30) REVERT: A 625 ASN cc_start: 0.9283 (t0) cc_final: 0.8531 (t0) REVERT: G 5 GLN cc_start: 0.8587 (tp-100) cc_final: 0.8368 (tp-100) REVERT: G 16 GLU cc_start: 0.8295 (pm20) cc_final: 0.7743 (pm20) REVERT: G 27 ASP cc_start: 0.9009 (t0) cc_final: 0.8761 (t0) REVERT: G 100 ASP cc_start: 0.8699 (t0) cc_final: 0.8401 (t0) REVERT: G 105 GLN cc_start: 0.9050 (pt0) cc_final: 0.8721 (pt0) REVERT: J 79 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7896 (mm-30) REVERT: J 100 GLN cc_start: 0.8926 (pm20) cc_final: 0.8723 (pm20) REVERT: F 166 ARG cc_start: 0.4368 (tpt170) cc_final: 0.1204 (tmt170) REVERT: C 621 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7914 (tm-30) REVERT: C 657 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8589 (tm-30) REVERT: C 659 ASP cc_start: 0.8695 (t0) cc_final: 0.8300 (m-30) REVERT: I 5 GLN cc_start: 0.8481 (tp-100) cc_final: 0.8134 (tp40) REVERT: I 27 ASP cc_start: 0.9246 (t70) cc_final: 0.8916 (t0) REVERT: I 72 ASP cc_start: 0.8673 (t70) cc_final: 0.8241 (t0) REVERT: I 100 ASP cc_start: 0.8486 (t70) cc_final: 0.8026 (t70) REVERT: K 24 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7834 (tmm160) outliers start: 48 outliers final: 43 residues processed: 263 average time/residue: 0.4228 time to fit residues: 172.0879 Evaluate side-chains 256 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 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 11 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 70 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 152 optimal weight: 6.9990 chunk 85 optimal weight: 0.0470 chunk 2 optimal weight: 10.0000 chunk 239 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.3684 ------------------------------------------------------------------------------- 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** ** 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 = 0.3200 r_free = 0.3200 target = 0.066941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.049647 restraints weight = 58170.034| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.88 r_work: 0.2661 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20892 Z= 0.203 Angle : 0.650 16.912 28533 Z= 0.313 Chirality : 0.046 0.446 3426 Planarity : 0.003 0.043 3477 Dihedral : 7.425 59.269 4479 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 2.38 % Allowed : 10.71 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2394 helix: 1.92 (0.28), residues: 396 sheet: -0.39 (0.18), residues: 816 loop : -1.04 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 571 HIS 0.006 0.001 HIS I 35B PHE 0.013 0.001 PHE D 53 TYR 0.019 0.001 TYR D 484 ARG 0.007 0.000 ARG F 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 60) link_NAG-ASN : angle 3.05703 ( 180) link_ALPHA1-6 : bond 0.00582 ( 3) link_ALPHA1-6 : angle 1.57625 ( 9) link_BETA1-4 : bond 0.00467 ( 24) link_BETA1-4 : angle 1.48624 ( 72) link_ALPHA1-3 : bond 0.01089 ( 3) link_ALPHA1-3 : angle 1.65855 ( 9) hydrogen bonds : bond 0.03920 ( 692) hydrogen bonds : angle 4.89757 ( 1977) SS BOND : bond 0.00298 ( 42) SS BOND : angle 0.67775 ( 84) covalent geometry : bond 0.00482 (20760) covalent geometry : angle 0.59973 (28179) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 2.845 Fit side-chains REVERT: E 475 MET cc_start: 0.9117 (mmm) cc_final: 0.8120 (mmm) REVERT: B 621 GLU cc_start: 0.8512 (tm-30) cc_final: 0.7886 (tm-30) REVERT: B 632 ASP cc_start: 0.9360 (t70) cc_final: 0.8929 (t0) REVERT: B 657 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8642 (tm-30) REVERT: H 46 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8241 (mt-10) REVERT: H 72 ASP cc_start: 0.8208 (t70) cc_final: 0.7293 (t0) REVERT: H 75 LYS cc_start: 0.9125 (mtmm) cc_final: 0.8676 (mtmm) REVERT: H 100 ASP cc_start: 0.8735 (t0) cc_final: 0.8337 (t0) REVERT: L 81 GLU cc_start: 0.7797 (pp20) cc_final: 0.7584 (pp20) REVERT: L 103 ARG cc_start: 0.7848 (ptm160) cc_final: 0.7438 (ptp-110) REVERT: D 36 VAL cc_start: 0.9373 (OUTLIER) cc_final: 0.9116 (p) REVERT: D 166 ARG cc_start: 0.4839 (ttt-90) cc_final: 0.4490 (ttt-90) REVERT: D 207 LYS cc_start: 0.7926 (tptp) cc_final: 0.7621 (tmtt) REVERT: A 621 GLU cc_start: 0.9043 (tt0) cc_final: 0.8402 (tm-30) REVERT: A 625 ASN cc_start: 0.9277 (t0) cc_final: 0.8510 (t0) REVERT: G 16 GLU cc_start: 0.8378 (pm20) cc_final: 0.7796 (pm20) REVERT: G 27 ASP cc_start: 0.9146 (t0) cc_final: 0.8902 (t0) REVERT: G 100 ASP cc_start: 0.8705 (t0) cc_final: 0.8404 (t0) REVERT: J 79 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8114 (mm-30) REVERT: F 166 ARG cc_start: 0.4578 (tpt170) cc_final: 0.1272 (tmt170) REVERT: C 621 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8144 (tm-30) REVERT: C 657 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8698 (tm-30) REVERT: I 5 GLN cc_start: 0.8555 (tp-100) cc_final: 0.8187 (tp40) REVERT: I 27 ASP cc_start: 0.9192 (t70) cc_final: 0.8911 (t0) REVERT: I 72 ASP cc_start: 0.8794 (t70) cc_final: 0.8376 (t0) REVERT: I 100 ASP cc_start: 0.8456 (t70) cc_final: 0.8044 (t70) REVERT: K 24 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8422 (mtp85) outliers start: 51 outliers final: 43 residues processed: 260 average time/residue: 0.4415 time to fit residues: 173.9985 Evaluate side-chains 256 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 224 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.066586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.049318 restraints weight = 58091.082| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.87 r_work: 0.2651 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20892 Z= 0.219 Angle : 0.665 16.602 28533 Z= 0.321 Chirality : 0.046 0.435 3426 Planarity : 0.004 0.043 3477 Dihedral : 7.389 59.552 4479 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.74 % Rotamer: Outliers : 2.57 % Allowed : 11.22 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2394 helix: 1.90 (0.28), residues: 396 sheet: -0.39 (0.18), residues: 816 loop : -1.04 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 571 HIS 0.006 0.001 HIS I 35B PHE 0.014 0.002 PHE D 53 TYR 0.020 0.001 TYR D 484 ARG 0.008 0.000 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 60) link_NAG-ASN : angle 3.04039 ( 180) link_ALPHA1-6 : bond 0.00515 ( 3) link_ALPHA1-6 : angle 1.57527 ( 9) link_BETA1-4 : bond 0.00487 ( 24) link_BETA1-4 : angle 1.45224 ( 72) link_ALPHA1-3 : bond 0.01051 ( 3) link_ALPHA1-3 : angle 1.57185 ( 9) hydrogen bonds : bond 0.03954 ( 692) hydrogen bonds : angle 4.88866 ( 1977) SS BOND : bond 0.00268 ( 42) SS BOND : angle 0.69808 ( 84) covalent geometry : bond 0.00521 (20760) covalent geometry : angle 0.61677 (28179) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 2.275 Fit side-chains REVERT: E 475 MET cc_start: 0.9130 (mmm) cc_final: 0.8135 (mmm) REVERT: B 621 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7873 (tm-30) REVERT: B 632 ASP cc_start: 0.9364 (t70) cc_final: 0.8926 (t0) REVERT: B 657 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8617 (tm-30) REVERT: H 46 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8152 (mt-10) REVERT: H 72 ASP cc_start: 0.8224 (t70) cc_final: 0.7315 (t0) REVERT: H 75 LYS cc_start: 0.9136 (mtmm) cc_final: 0.8675 (mtmm) REVERT: H 100 ASP cc_start: 0.8762 (t0) cc_final: 0.8386 (t0) REVERT: L 81 GLU cc_start: 0.7866 (pp20) cc_final: 0.7639 (pp20) REVERT: L 103 ARG cc_start: 0.7845 (ptm160) cc_final: 0.7433 (ptp-110) REVERT: D 166 ARG cc_start: 0.4877 (ttt-90) cc_final: 0.4494 (ttt-90) REVERT: D 207 LYS cc_start: 0.7952 (tptp) cc_final: 0.7648 (tmtt) REVERT: A 621 GLU cc_start: 0.9025 (tt0) cc_final: 0.8425 (tm-30) REVERT: A 625 ASN cc_start: 0.9320 (t0) cc_final: 0.8614 (t0) REVERT: A 632 ASP cc_start: 0.9275 (OUTLIER) cc_final: 0.8986 (t0) REVERT: G 16 GLU cc_start: 0.8349 (pm20) cc_final: 0.7976 (pm20) REVERT: G 27 ASP cc_start: 0.9165 (t0) cc_final: 0.8914 (t0) REVERT: G 100 ASP cc_start: 0.8685 (t0) cc_final: 0.8389 (t0) REVERT: J 79 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8136 (mm-30) REVERT: J 102 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7707 (t) REVERT: F 166 ARG cc_start: 0.4561 (tpt170) cc_final: 0.1080 (tmt170) REVERT: C 621 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8276 (tm-30) REVERT: C 632 ASP cc_start: 0.9209 (t70) cc_final: 0.8803 (t0) REVERT: C 657 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8711 (tm-30) REVERT: C 659 ASP cc_start: 0.8786 (t0) cc_final: 0.8445 (m-30) REVERT: I 5 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8205 (tp40) REVERT: I 27 ASP cc_start: 0.9184 (t70) cc_final: 0.8888 (t0) REVERT: I 72 ASP cc_start: 0.8812 (t70) cc_final: 0.8398 (t0) REVERT: I 100 ASP cc_start: 0.8486 (t70) cc_final: 0.8090 (t70) REVERT: K 24 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8416 (mtp85) outliers start: 55 outliers final: 47 residues processed: 264 average time/residue: 0.4718 time to fit residues: 191.3631 Evaluate side-chains 269 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 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 488 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 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 9 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 23 optimal weight: 5.9990 chunk 158 optimal weight: 0.0670 chunk 20 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 214 optimal weight: 0.1980 chunk 3 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.8524 ------------------------------------------------------------------------------- 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 = 0.3181 r_free = 0.3181 target = 0.066088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.048786 restraints weight = 58469.962| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.88 r_work: 0.2635 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3641 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= 0.238 Angle : 0.681 16.443 28533 Z= 0.330 Chirality : 0.047 0.420 3426 Planarity : 0.004 0.044 3477 Dihedral : 7.405 59.706 4479 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.39 % Favored : 95.57 % Rotamer: Outliers : 2.71 % Allowed : 11.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.17), residues: 2394 helix: 1.86 (0.28), residues: 396 sheet: -0.40 (0.18), residues: 819 loop : -1.06 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 571 HIS 0.006 0.001 HIS F 105 PHE 0.015 0.002 PHE I 91 TYR 0.018 0.001 TYR D 484 ARG 0.006 0.000 ARG J 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 60) link_NAG-ASN : angle 3.05742 ( 180) link_ALPHA1-6 : bond 0.00416 ( 3) link_ALPHA1-6 : angle 1.56033 ( 9) link_BETA1-4 : bond 0.00478 ( 24) link_BETA1-4 : angle 1.46344 ( 72) link_ALPHA1-3 : bond 0.00962 ( 3) link_ALPHA1-3 : angle 1.47522 ( 9) hydrogen bonds : bond 0.04078 ( 692) hydrogen bonds : angle 4.89641 ( 1977) SS BOND : bond 0.00278 ( 42) SS BOND : angle 0.74566 ( 84) covalent geometry : bond 0.00567 (20760) covalent geometry : angle 0.63345 (28179) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 222 time to evaluate : 5.960 Fit side-chains revert: symmetry clash REVERT: E 475 MET cc_start: 0.9111 (mmm) cc_final: 0.8095 (mmm) REVERT: B 621 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7852 (tm-30) REVERT: B 632 ASP cc_start: 0.9357 (t70) cc_final: 0.8915 (t0) REVERT: B 657 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8507 (tm-30) REVERT: H 46 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8092 (mt-10) REVERT: H 100 ASP cc_start: 0.8820 (t0) cc_final: 0.8436 (t0) REVERT: L 81 GLU cc_start: 0.7927 (pp20) cc_final: 0.7678 (pp20) REVERT: D 166 ARG cc_start: 0.4806 (ttt-90) cc_final: 0.4396 (ttt-90) REVERT: D 207 LYS cc_start: 0.7999 (tptp) cc_final: 0.7710 (tmtt) REVERT: A 621 GLU cc_start: 0.8998 (tt0) cc_final: 0.8379 (tm-30) REVERT: A 625 ASN cc_start: 0.9317 (t0) cc_final: 0.8544 (t0) REVERT: A 632 ASP cc_start: 0.9287 (OUTLIER) cc_final: 0.9012 (t0) REVERT: G 16 GLU cc_start: 0.8309 (pm20) cc_final: 0.7981 (pm20) REVERT: G 27 ASP cc_start: 0.9177 (t0) cc_final: 0.8909 (t0) REVERT: G 100 ASP cc_start: 0.8710 (t0) cc_final: 0.8402 (t0) REVERT: J 79 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8168 (mm-30) REVERT: J 102 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7655 (t) REVERT: F 166 ARG cc_start: 0.4542 (tpt170) cc_final: 0.1092 (tmt170) REVERT: C 621 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8227 (tm-30) REVERT: C 657 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8714 (tm-30) REVERT: I 27 ASP cc_start: 0.9192 (t70) cc_final: 0.8915 (t0) REVERT: I 72 ASP cc_start: 0.8821 (t70) cc_final: 0.8413 (t0) REVERT: I 100 ILE cc_start: 0.9406 (mm) cc_final: 0.9098 (mm) REVERT: I 100 ASP cc_start: 0.8575 (t70) cc_final: 0.8164 (t70) REVERT: K 24 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7935 (tmm160) outliers start: 58 outliers final: 48 residues processed: 266 average time/residue: 0.5366 time to fit residues: 224.4853 Evaluate side-chains 267 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 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 9 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 82 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 125 optimal weight: 0.0050 chunk 13 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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** ** 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 = 0.3235 r_free = 0.3235 target = 0.071058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.052622 restraints weight = 59580.181| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.94 r_work: 0.2688 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20892 Z= 0.116 Angle : 0.618 17.493 28533 Z= 0.295 Chirality : 0.044 0.401 3426 Planarity : 0.003 0.041 3477 Dihedral : 7.037 59.323 4479 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.09 % Favored : 96.87 % Rotamer: Outliers : 2.15 % Allowed : 12.39 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2394 helix: 2.01 (0.28), residues: 396 sheet: -0.27 (0.18), residues: 819 loop : -0.97 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 571 HIS 0.006 0.001 HIS I 35B PHE 0.010 0.001 PHE D 53 TYR 0.018 0.001 TYR D 484 ARG 0.007 0.000 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 60) link_NAG-ASN : angle 2.94452 ( 180) link_ALPHA1-6 : bond 0.00519 ( 3) link_ALPHA1-6 : angle 1.44430 ( 9) link_BETA1-4 : bond 0.00495 ( 24) link_BETA1-4 : angle 1.28238 ( 72) link_ALPHA1-3 : bond 0.01023 ( 3) link_ALPHA1-3 : angle 1.22482 ( 9) hydrogen bonds : bond 0.03360 ( 692) hydrogen bonds : angle 4.67762 ( 1977) SS BOND : bond 0.00192 ( 42) SS BOND : angle 0.51817 ( 84) covalent geometry : bond 0.00264 (20760) covalent geometry : angle 0.57033 (28179) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 3.120 Fit side-chains REVERT: E 475 MET cc_start: 0.9115 (mmm) cc_final: 0.8050 (mmm) REVERT: B 621 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8031 (tm-30) REVERT: B 632 ASP cc_start: 0.9311 (t70) cc_final: 0.8829 (t0) REVERT: B 657 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8481 (tm-30) REVERT: H 46 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7964 (mt-10) REVERT: H 75 LYS cc_start: 0.9251 (mtmm) cc_final: 0.8906 (mtmm) REVERT: H 86 ASP cc_start: 0.8753 (m-30) cc_final: 0.8384 (m-30) REVERT: H 100 ASP cc_start: 0.8738 (t0) cc_final: 0.8324 (t0) REVERT: L 81 GLU cc_start: 0.7917 (pp20) cc_final: 0.7675 (pp20) REVERT: D 166 ARG cc_start: 0.4782 (ttt-90) cc_final: 0.4409 (ttt-90) REVERT: D 207 LYS cc_start: 0.7905 (tptp) cc_final: 0.7623 (tmtt) REVERT: D 475 MET cc_start: 0.8321 (mmm) cc_final: 0.7824 (mmt) REVERT: A 625 ASN cc_start: 0.9303 (t0) cc_final: 0.8751 (t0) REVERT: A 632 ASP cc_start: 0.9227 (OUTLIER) cc_final: 0.8948 (t0) REVERT: G 5 GLN cc_start: 0.8635 (tp-100) cc_final: 0.8334 (tp-100) REVERT: G 16 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: G 27 ASP cc_start: 0.9126 (t0) cc_final: 0.8544 (t0) REVERT: G 100 ASP cc_start: 0.8545 (t0) cc_final: 0.8259 (t0) REVERT: J 79 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8105 (mm-30) REVERT: J 100 GLN cc_start: 0.8758 (pm20) cc_final: 0.8518 (pm20) REVERT: F 166 ARG cc_start: 0.4426 (tpt170) cc_final: 0.1584 (ttt90) REVERT: C 621 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8196 (tm-30) REVERT: C 659 ASP cc_start: 0.8748 (t0) cc_final: 0.8417 (m-30) REVERT: I 27 ASP cc_start: 0.9192 (t70) cc_final: 0.8886 (t0) REVERT: I 72 ASP cc_start: 0.8806 (t70) cc_final: 0.8392 (t0) REVERT: I 100 ILE cc_start: 0.9372 (mm) cc_final: 0.9040 (mm) REVERT: I 100 ASP cc_start: 0.8351 (t70) cc_final: 0.7910 (t70) REVERT: K 24 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8381 (mtp85) outliers start: 46 outliers final: 38 residues processed: 267 average time/residue: 0.6620 time to fit residues: 280.5951 Evaluate side-chains 265 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 58 VAL 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 229 optimal weight: 0.2980 chunk 168 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3197 r_free = 0.3197 target = 0.067762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.050249 restraints weight = 57336.841| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.93 r_work: 0.2693 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20892 Z= 0.117 Angle : 0.613 17.017 28533 Z= 0.293 Chirality : 0.044 0.387 3426 Planarity : 0.003 0.042 3477 Dihedral : 6.847 56.182 4479 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.41 % Rotamer: Outliers : 2.06 % Allowed : 12.39 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), residues: 2394 helix: 2.02 (0.28), residues: 396 sheet: -0.16 (0.18), residues: 813 loop : -0.94 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 571 HIS 0.005 0.001 HIS I 35B PHE 0.009 0.001 PHE F 53 TYR 0.020 0.001 TYR D 484 ARG 0.006 0.000 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 60) link_NAG-ASN : angle 2.83680 ( 180) link_ALPHA1-6 : bond 0.00416 ( 3) link_ALPHA1-6 : angle 1.50751 ( 9) link_BETA1-4 : bond 0.00508 ( 24) link_BETA1-4 : angle 1.33731 ( 72) link_ALPHA1-3 : bond 0.00983 ( 3) link_ALPHA1-3 : angle 1.32442 ( 9) hydrogen bonds : bond 0.03272 ( 692) hydrogen bonds : angle 4.59166 ( 1977) SS BOND : bond 0.00172 ( 42) SS BOND : angle 0.51844 ( 84) covalent geometry : bond 0.00271 (20760) covalent geometry : angle 0.56792 (28179) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 233 time to evaluate : 2.761 Fit side-chains REVERT: E 475 MET cc_start: 0.9131 (mmm) cc_final: 0.8059 (mmm) REVERT: B 621 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8085 (tm-30) REVERT: B 632 ASP cc_start: 0.9307 (t70) cc_final: 0.8824 (t0) REVERT: B 657 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8500 (tm-30) REVERT: H 46 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7940 (mt-10) REVERT: H 75 LYS cc_start: 0.9233 (mtmm) cc_final: 0.8855 (mtmm) REVERT: H 86 ASP cc_start: 0.8802 (m-30) cc_final: 0.8481 (m-30) REVERT: H 100 ASP cc_start: 0.8761 (t0) cc_final: 0.8309 (t0) REVERT: L 81 GLU cc_start: 0.7934 (pp20) cc_final: 0.7690 (pp20) REVERT: D 166 ARG cc_start: 0.4779 (ttt-90) cc_final: 0.4384 (ttt-90) REVERT: D 207 LYS cc_start: 0.7885 (tptp) cc_final: 0.7610 (tmtt) REVERT: D 475 MET cc_start: 0.8364 (mmm) cc_final: 0.7900 (mmt) REVERT: A 621 GLU cc_start: 0.8899 (tt0) cc_final: 0.8353 (tm-30) REVERT: A 625 ASN cc_start: 0.9238 (t0) cc_final: 0.8595 (t0) REVERT: A 632 ASP cc_start: 0.9224 (OUTLIER) cc_final: 0.8935 (t0) REVERT: G 5 GLN cc_start: 0.8599 (tp-100) cc_final: 0.8384 (tp-100) REVERT: G 16 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: G 27 ASP cc_start: 0.9099 (t0) cc_final: 0.8512 (t0) REVERT: G 100 ASP cc_start: 0.8571 (t0) cc_final: 0.8296 (t0) REVERT: J 79 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8099 (mm-30) REVERT: J 82 ASP cc_start: 0.8336 (m-30) cc_final: 0.8131 (m-30) REVERT: F 166 ARG cc_start: 0.4409 (tpt170) cc_final: 0.0717 (ttt-90) REVERT: C 621 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8244 (tm-30) REVERT: C 659 ASP cc_start: 0.8747 (t0) cc_final: 0.8426 (m-30) REVERT: I 27 ASP cc_start: 0.9185 (t70) cc_final: 0.8859 (t0) REVERT: I 72 ASP cc_start: 0.8801 (t70) cc_final: 0.8391 (t0) REVERT: I 100 ILE cc_start: 0.9369 (mm) cc_final: 0.9052 (mm) REVERT: I 100 ASP cc_start: 0.8341 (t70) cc_final: 0.7904 (t70) outliers start: 44 outliers final: 37 residues processed: 263 average time/residue: 0.3645 time to fit residues: 145.5046 Evaluate side-chains 267 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 228 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain D residue 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 488 VAL 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 16 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 196 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 59 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 chunk 188 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.067429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.049901 restraints weight = 57735.507| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.93 r_work: 0.2683 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20892 Z= 0.139 Angle : 0.618 16.610 28533 Z= 0.295 Chirality : 0.044 0.382 3426 Planarity : 0.003 0.041 3477 Dihedral : 6.817 56.521 4479 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.47 % Favored : 96.49 % Rotamer: Outliers : 1.92 % Allowed : 12.67 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.17), residues: 2394 helix: 2.02 (0.28), residues: 399 sheet: -0.17 (0.18), residues: 819 loop : -0.97 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 571 HIS 0.005 0.001 HIS I 35B PHE 0.010 0.001 PHE F 53 TYR 0.021 0.001 TYR D 484 ARG 0.006 0.000 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 60) link_NAG-ASN : angle 2.82276 ( 180) link_ALPHA1-6 : bond 0.00393 ( 3) link_ALPHA1-6 : angle 1.53056 ( 9) link_BETA1-4 : bond 0.00499 ( 24) link_BETA1-4 : angle 1.33397 ( 72) link_ALPHA1-3 : bond 0.00868 ( 3) link_ALPHA1-3 : angle 1.26406 ( 9) hydrogen bonds : bond 0.03323 ( 692) hydrogen bonds : angle 4.55306 ( 1977) SS BOND : bond 0.00194 ( 42) SS BOND : angle 0.54646 ( 84) covalent geometry : bond 0.00329 (20760) covalent geometry : angle 0.57319 (28179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15465.99 seconds wall clock time: 280 minutes 24.43 seconds (16824.43 seconds total)