Starting phenix.real_space_refine on Fri Aug 7 08:23:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yhr_72971/08_2026/9yhr_72971.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yhr_72971/08_2026/9yhr_72971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yhr_72971/08_2026/9yhr_72971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yhr_72971/08_2026/9yhr_72971.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yhr_72971/08_2026/9yhr_72971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yhr_72971/08_2026/9yhr_72971.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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 12468 2.51 5 N 3291 2.21 5 O 3996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19875 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "B" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 23, 'TRANS': 413} Chain breaks: 4 Chain: "F" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 23, 'TRANS': 413} Chain breaks: 4 Chain: "G" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 23, 'TRANS': 413} Chain breaks: 4 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 937 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 2 Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 937 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 2 Chain: "K" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "L" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 937 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 2 Chain: "N" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "D" 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: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Q" Number of atoms: 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: "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: "G" 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 Time building chain proxies: 4.28, per 1000 atoms: 0.22 Number of scatterers: 19875 At special positions: 0 Unit cell: (157.248, 156.416, 143.104, 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 3996 8.00 N 3291 7.00 C 12468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS G 501 " distance=2.03 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 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=2.03 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 G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 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 ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN P 5 " - " MAN P 6 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN Z 4 " - " MAN Z 5 " " MAN Z 5 " - " MAN Z 6 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA P 3 " - " MAN P 7 " " BMA U 3 " - " MAN U 7 " " BMA Z 3 " - " MAN Z 7 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " 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 R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " 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-ASN " NAG A 701 " - " ASN A 611 " " NAG B 701 " - " ASN B 611 " " NAG C 701 " - " ASN C 611 " " NAG D 1 " - " ASN E 234 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 156 " " NAG E 604 " - " ASN E 160 " " NAG E 605 " - " ASN E 197 " " NAG E 606 " - " ASN E 230 " " NAG E 607 " - " ASN E 241 " " NAG E 608 " - " ASN E 276 " " NAG E 609 " - " ASN E 301 " " NAG E 610 " - " ASN E 339 " " NAG E 611 " - " ASN E 344 " " NAG E 612 " - " ASN E 392 " " NAG E 613 " - " ASN E 448 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 160 " " NAG F 605 " - " ASN F 197 " " NAG F 606 " - " ASN F 230 " " NAG F 607 " - " ASN F 241 " " NAG F 608 " - " ASN F 276 " " NAG F 609 " - " ASN F 301 " " NAG F 610 " - " ASN F 339 " " NAG F 611 " - " ASN F 344 " " NAG F 612 " - " ASN F 392 " " NAG F 613 " - " ASN F 448 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 156 " " NAG G 604 " - " ASN G 160 " " NAG G 605 " - " ASN G 197 " " NAG G 606 " - " ASN G 230 " " NAG G 607 " - " ASN G 241 " " NAG G 608 " - " ASN G 276 " " NAG G 609 " - " ASN G 301 " " NAG G 610 " - " ASN G 339 " " NAG G 611 " - " ASN G 344 " " NAG G 612 " - " ASN G 392 " " NAG G 613 " - " ASN G 448 " " NAG I 1 " - " ASN E 262 " " NAG O 1 " - " ASN E 295 " " NAG P 1 " - " ASN E 332 " " NAG Q 1 " - " ASN E 386 " " NAG R 1 " - " ASN F 234 " " NAG S 1 " - " ASN F 262 " " NAG T 1 " - " ASN F 295 " " NAG U 1 " - " ASN F 332 " " NAG V 1 " - " ASN F 386 " " NAG W 1 " - " ASN G 234 " " NAG X 1 " - " ASN G 262 " " NAG Y 1 " - " ASN G 295 " " NAG Z 1 " - " ASN G 332 " " NAG a 1 " - " ASN G 386 " Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 539.0 milliseconds 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4374 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 42 sheets defined 19.1% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... 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: 4.135A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 596 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 650 removed outlier: 3.520A pdb=" N ILE A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 664 removed outlier: 3.900A pdb=" N ASP A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.090A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.521A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 664 removed outlier: 3.900A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 543 removed outlier: 4.089A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 650 removed outlier: 3.521A pdb=" N ILE C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 664 removed outlier: 3.900A pdb=" N ASP C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.628A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 474 through 483 removed outlier: 4.047A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 353 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.627A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 425 through 429' Processing helix chain 'F' and resid 474 through 483 removed outlier: 4.048A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 117 Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.627A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 474 through 483 removed outlier: 4.048A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.692A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.910A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.691A pdb=" N LYS J 64 " --> pdb=" O PRO J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.910A pdb=" N THR J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 removed outlier: 3.691A pdb=" N LYS M 64 " --> pdb=" O PRO M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.911A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 604 through 609 removed outlier: 4.467A pdb=" N VAL E 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 604 through 609 removed outlier: 4.468A pdb=" N VAL F 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 604 through 609 removed outlier: 4.468A pdb=" N VAL G 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.802A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 55 removed outlier: 3.993A pdb=" N PHE E 53 " --> pdb=" O CYS E 218 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS E 218 " --> pdb=" O PHE E 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AA7, first strand: chain 'E' and resid 169 through 174 Processing sheet with id=AA8, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.366A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.858A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.006A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.277A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.006A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.858A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 301 through 308 removed outlier: 6.719A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AB3, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.803A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 53 through 55 removed outlier: 3.992A pdb=" N PHE F 53 " --> pdb=" O CYS F 218 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS F 218 " --> pdb=" O PHE F 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 91 through 93 Processing sheet with id=AB6, first strand: chain 'F' and resid 169 through 174 Processing sheet with id=AB7, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.366A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 11.857A pdb=" N ILE F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.877A pdb=" N LEU F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 11.006A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.276A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS F 421 " --> pdb=" O PHE F 382 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.276A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 11.006A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.877A pdb=" N LEU F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 11.857A pdb=" N ILE F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 301 through 308 removed outlier: 6.719A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.803A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 55 removed outlier: 3.992A pdb=" N PHE G 53 " --> pdb=" O CYS G 218 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS G 218 " --> pdb=" O PHE G 53 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 91 through 93 Processing sheet with id=AC5, first strand: chain 'G' and resid 169 through 174 Processing sheet with id=AC6, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.366A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.859A pdb=" N ILE G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 11.877A pdb=" N LEU G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.006A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 271 through 273 removed outlier: 11.277A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 11.006A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.877A pdb=" N LEU G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.859A pdb=" N ILE G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 301 through 308 removed outlier: 6.719A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.686A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.852A pdb=" N TRP H 35A" --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N TYR H 52 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TYR H 34 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL H 102 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.686A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.852A pdb=" N TRP H 35A" --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N TYR H 52 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TYR H 34 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.686A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SER J 50 " --> pdb=" O TRP J 35A" (cutoff:3.500A) removed outlier: 6.852A pdb=" N TRP J 35A" --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N TYR J 52 " --> pdb=" O TYR J 34 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR J 34 " --> pdb=" O TYR J 52 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL J 102 " --> pdb=" O SER J 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.686A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SER J 50 " --> pdb=" O TRP J 35A" (cutoff:3.500A) removed outlier: 6.852A pdb=" N TRP J 35A" --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N TYR J 52 " --> pdb=" O TYR J 34 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR J 34 " --> pdb=" O TYR J 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.507A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY K 84 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.508A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.685A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER M 50 " --> pdb=" O TRP M 35A" (cutoff:3.500A) removed outlier: 6.852A pdb=" N TRP M 35A" --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR M 52 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TYR M 34 " --> pdb=" O TYR M 52 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL M 102 " --> pdb=" O SER M 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.685A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER M 50 " --> pdb=" O TRP M 35A" (cutoff:3.500A) removed outlier: 6.852A pdb=" N TRP M 35A" --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR M 52 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TYR M 34 " --> pdb=" O TYR M 52 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.508A pdb=" N LEU N 11 " --> pdb=" O ASP N 105 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY N 84 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 741 hydrogen bonds defined for protein. 1998 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 2.39 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: 6054 1.34 - 1.46: 3701 1.46 - 1.57: 10393 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 20304 Sorted by residual: bond pdb=" C1 MAN X 4 " pdb=" O5 MAN X 4 " ideal model delta sigma weight residual 1.399 1.451 -0.052 2.00e-02 2.50e+03 6.78e+00 bond pdb=" C1 MAN S 4 " pdb=" O5 MAN S 4 " ideal model delta sigma weight residual 1.399 1.451 -0.052 2.00e-02 2.50e+03 6.77e+00 bond pdb=" C1 MAN I 4 " pdb=" O5 MAN I 4 " ideal model delta sigma weight residual 1.399 1.450 -0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" C3 BMA X 3 " pdb=" O3 BMA X 3 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" C1 MAN Z 5 " pdb=" O5 MAN Z 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.57e+00 ... (remaining 20299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 26715 1.70 - 3.40: 732 3.40 - 5.10: 105 5.10 - 6.80: 33 6.80 - 8.50: 6 Bond angle restraints: 27591 Sorted by residual: angle pdb=" C LEU A 602 " pdb=" CA LEU A 602 " pdb=" CB LEU A 602 " ideal model delta sigma weight residual 116.34 111.05 5.29 1.40e+00 5.10e-01 1.43e+01 angle pdb=" C LEU B 602 " pdb=" CA LEU B 602 " pdb=" CB LEU B 602 " ideal model delta sigma weight residual 116.34 111.07 5.27 1.40e+00 5.10e-01 1.42e+01 angle pdb=" C LEU C 602 " pdb=" CA LEU C 602 " pdb=" CB LEU C 602 " ideal model delta sigma weight residual 116.34 111.07 5.27 1.40e+00 5.10e-01 1.42e+01 angle pdb=" N ILE C 573 " pdb=" CA ILE C 573 " pdb=" C ILE C 573 " ideal model delta sigma weight residual 112.96 109.28 3.68 1.00e+00 1.00e+00 1.35e+01 angle pdb=" N ILE A 573 " pdb=" CA ILE A 573 " pdb=" C ILE A 573 " ideal model delta sigma weight residual 112.96 109.30 3.66 1.00e+00 1.00e+00 1.34e+01 ... (remaining 27586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 12233 21.67 - 43.34: 877 43.34 - 65.01: 105 65.01 - 86.68: 57 86.68 - 108.35: 27 Dihedral angle restraints: 13299 sinusoidal: 6489 harmonic: 6810 Sorted by residual: 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 -140.05 54.05 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -140.05 54.05 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -140.04 54.04 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 13296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2798 0.069 - 0.139: 487 0.139 - 0.208: 33 0.208 - 0.278: 0 0.278 - 0.347: 12 Chirality restraints: 3330 Sorted by residual: chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.62 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.62 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C5 BMA Z 3 " pdb=" C4 BMA Z 3 " pdb=" C6 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.62 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 3327 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 100G" -0.091 9.50e-02 1.11e+02 4.09e-02 1.04e+00 pdb=" NE ARG J 100G" 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG J 100G" -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG J 100G" 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG J 100G" -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 100G" -0.091 9.50e-02 1.11e+02 4.07e-02 1.03e+00 pdb=" NE ARG M 100G" 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG M 100G" -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG M 100G" 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG M 100G" -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 100G" -0.090 9.50e-02 1.11e+02 4.05e-02 1.02e+00 pdb=" NE ARG H 100G" 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG H 100G" -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG H 100G" 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 100G" -0.003 2.00e-02 2.50e+03 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.08: 12776 3.08 - 3.53: 18794 3.53 - 3.99: 30010 3.99 - 4.44: 35739 4.44 - 4.90: 57461 Nonbonded interactions: 154780 Sorted by model distance: nonbonded pdb=" C4 BMA U 3 " pdb=" O6 BMA U 3 " model vdw 2.621 2.776 nonbonded pdb=" C4 BMA Z 3 " pdb=" O6 BMA Z 3 " model vdw 2.621 2.776 nonbonded pdb=" C4 BMA P 3 " pdb=" O6 BMA P 3 " model vdw 2.622 2.776 nonbonded pdb=" CB THR E 464 " pdb=" N THR E 465 " model vdw 2.635 2.840 nonbonded pdb=" CB THR F 464 " pdb=" N THR F 465 " model vdw 2.635 2.840 ... (remaining 154775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'a' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'S' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.960 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.005 0.052 20439 Z= 0.226 Angle : 0.704 12.888 27954 Z= 0.303 Chirality : 0.052 0.347 3330 Planarity : 0.003 0.041 3399 Dihedral : 15.350 108.345 8799 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.29 % Allowed : 7.34 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.18), residues: 2301 helix: 1.74 (0.28), residues: 390 sheet: 0.71 (0.20), residues: 669 loop : -0.55 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 100G TYR 0.011 0.001 TYR H 52 PHE 0.011 0.001 PHE F 53 TRP 0.006 0.001 TRP G 96 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.22 (20304) covalent geometry : angle 0.63433 / 0.29 (27591) SS BOND : bond 0.00192 / 0.12 ( 42) SS BOND : angle 0.40221 / 0.29 ( 84) hydrogen bonds : bond 0.09526 / 6.12 ( 684) hydrogen bonds : angle 6.02132 / 4.21 ( 1998) link_ALPHA1-2 : bond 0.00310 / 0.16 ( 6) link_ALPHA1-2 : angle 1.38384 / 0.74 ( 18) link_ALPHA1-3 : bond 0.02714 / 1.55 ( 6) link_ALPHA1-3 : angle 6.36622 / 4.12 ( 18) link_ALPHA1-6 : bond 0.00102 / 0.05 ( 3) link_ALPHA1-6 : angle 0.84540 / 0.42 ( 9) link_BETA1-4 : bond 0.00845 / 0.52 ( 21) link_BETA1-4 : angle 2.02374 / 1.42 ( 63) link_NAG-ASN : bond 0.00375 / 0.24 ( 57) link_NAG-ASN : angle 3.16879 / 2.05 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 394 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 625 ASN cc_start: 0.7372 (m-40) cc_final: 0.7028 (t0) REVERT: E 97 LYS cc_start: 0.8369 (mtmm) cc_final: 0.8136 (mmmm) REVERT: E 104 MET cc_start: 0.8702 (ttt) cc_final: 0.8460 (ttt) REVERT: E 114 GLN cc_start: 0.7828 (tt0) cc_final: 0.7147 (mm-40) REVERT: E 142 MET cc_start: 0.5766 (ttm) cc_final: 0.5335 (tpp) REVERT: E 167 ASP cc_start: 0.8769 (m-30) cc_final: 0.8468 (m-30) REVERT: E 189 LYS cc_start: 0.7468 (mmtm) cc_final: 0.6970 (mmmt) REVERT: E 289 ASN cc_start: 0.8809 (p0) cc_final: 0.8526 (p0) REVERT: E 419 ARG cc_start: 0.8006 (mtm-85) cc_final: 0.7738 (mtp85) REVERT: F 97 LYS cc_start: 0.8316 (mtmm) cc_final: 0.8094 (mmmm) REVERT: F 114 GLN cc_start: 0.7809 (tt0) cc_final: 0.7135 (mm-40) REVERT: F 189 LYS cc_start: 0.7488 (mmtm) cc_final: 0.6816 (mmmt) REVERT: F 246 GLN cc_start: 0.5721 (tp-100) cc_final: 0.5399 (tt0) REVERT: G 92 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7860 (mp0) REVERT: G 104 MET cc_start: 0.8526 (ttt) cc_final: 0.8276 (ttt) REVERT: G 114 GLN cc_start: 0.7649 (tt0) cc_final: 0.7008 (mm-40) REVERT: G 189 LYS cc_start: 0.7438 (mmtm) cc_final: 0.6744 (mmmt) REVERT: G 289 ASN cc_start: 0.8843 (p0) cc_final: 0.8463 (p0) REVERT: G 444 ARG cc_start: 0.8206 (mtm-85) cc_final: 0.7976 (mtm-85) REVERT: H 101 ASP cc_start: 0.7031 (m-30) cc_final: 0.6699 (m-30) REVERT: J 101 ASP cc_start: 0.7541 (m-30) cc_final: 0.7043 (m-30) REVERT: L 39 LYS cc_start: 0.7831 (mtpp) cc_final: 0.7572 (mtmt) REVERT: M 33 TYR cc_start: 0.8435 (m-10) cc_final: 0.8104 (m-80) REVERT: N 23 CYS cc_start: 0.7201 (t) cc_final: 0.6976 (t) REVERT: N 54 ARG cc_start: 0.8492 (ttm110) cc_final: 0.8289 (ttp-110) REVERT: N 79 GLU cc_start: 0.8227 (mt-10) cc_final: 0.8027 (mt-10) outliers start: 6 outliers final: 3 residues processed: 399 average time/residue: 0.1562 time to fit residues: 93.8167 Evaluate side-chains 262 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 259 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain G residue 126 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 GLN A 590 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 GLN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN E 103 GLN E 105 HIS E 352 HIS F 103 GLN F 105 HIS G 103 GLN G 105 HIS G 352 HIS K 27DHIS K 90 GLN L 90 GLN N 90 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.144179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111134 restraints weight = 27682.150| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.08 r_work: 0.3218 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20439 Z= 0.138 Angle : 0.651 13.190 27954 Z= 0.296 Chirality : 0.050 0.603 3330 Planarity : 0.003 0.063 3399 Dihedral : 8.972 70.655 4452 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.77 % Allowed : 12.23 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.18), residues: 2301 helix: 1.83 (0.28), residues: 393 sheet: 0.64 (0.21), residues: 642 loop : -0.58 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 444 TYR 0.011 0.001 TYR J 52 PHE 0.015 0.001 PHE G 53 TRP 0.013 0.001 TRP H 103 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (20304) covalent geometry : angle 0.56826 / 0.28 (27591) SS BOND : bond 0.00289 / 0.17 ( 42) SS BOND : angle 1.06437 / 0.70 ( 84) hydrogen bonds : bond 0.03270 / 2.11 ( 684) hydrogen bonds : angle 4.73867 / 3.34 ( 1998) link_ALPHA1-2 : bond 0.00617 / 0.33 ( 6) link_ALPHA1-2 : angle 1.63552 / 0.96 ( 18) link_ALPHA1-3 : bond 0.02883 / 1.65 ( 6) link_ALPHA1-3 : angle 3.81668 / 2.31 ( 18) link_ALPHA1-6 : bond 0.00708 / 0.36 ( 3) link_ALPHA1-6 : angle 1.11009 / 0.63 ( 9) link_BETA1-4 : bond 0.00598 / 0.36 ( 21) link_BETA1-4 : angle 2.34829 / 1.52 ( 63) link_NAG-ASN : bond 0.00442 / 0.28 ( 57) link_NAG-ASN : angle 3.57278 / 2.42 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 269 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 625 ASN cc_start: 0.7433 (m-40) cc_final: 0.6845 (t0) REVERT: E 97 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8054 (mmmm) REVERT: E 102 GLU cc_start: 0.7765 (mp0) cc_final: 0.7374 (mp0) REVERT: E 104 MET cc_start: 0.8687 (ttt) cc_final: 0.8470 (ttt) REVERT: E 114 GLN cc_start: 0.7762 (tt0) cc_final: 0.7055 (mm-40) REVERT: E 167 ASP cc_start: 0.8738 (m-30) cc_final: 0.8417 (m-30) REVERT: E 189 LYS cc_start: 0.7390 (mmtm) cc_final: 0.6817 (mmmt) REVERT: E 289 ASN cc_start: 0.8878 (p0) cc_final: 0.8610 (p0) REVERT: F 46 LYS cc_start: 0.8277 (mmtp) cc_final: 0.7765 (mttt) REVERT: F 97 LYS cc_start: 0.8311 (mtmm) cc_final: 0.8064 (mmmm) REVERT: F 102 GLU cc_start: 0.7843 (mp0) cc_final: 0.7422 (mp0) REVERT: F 114 GLN cc_start: 0.7761 (tt0) cc_final: 0.7067 (mm-40) REVERT: F 189 LYS cc_start: 0.7430 (mmtm) cc_final: 0.6684 (mmmt) REVERT: F 246 GLN cc_start: 0.5856 (tp-100) cc_final: 0.5467 (tt0) REVERT: G 92 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7749 (mp0) REVERT: G 102 GLU cc_start: 0.7910 (mp0) cc_final: 0.7514 (mp0) REVERT: G 114 GLN cc_start: 0.7646 (tt0) cc_final: 0.6941 (mm-40) REVERT: G 189 LYS cc_start: 0.7405 (mmtm) cc_final: 0.6646 (mmmt) REVERT: G 289 ASN cc_start: 0.8917 (p0) cc_final: 0.8555 (p0) REVERT: G 321 ASP cc_start: 0.7755 (t0) cc_final: 0.7507 (p0) REVERT: G 444 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.8141 (mtt-85) REVERT: H 101 ASP cc_start: 0.7072 (m-30) cc_final: 0.6760 (m-30) REVERT: L 39 LYS cc_start: 0.7677 (mtpp) cc_final: 0.7296 (mtmt) REVERT: L 90 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: N 23 CYS cc_start: 0.6466 (t) cc_final: 0.6040 (t) REVERT: N 54 ARG cc_start: 0.8456 (ttm110) cc_final: 0.8031 (ttp-110) REVERT: N 79 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7516 (mt-10) REVERT: N 90 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7386 (tt0) outliers start: 37 outliers final: 25 residues processed: 284 average time/residue: 0.1498 time to fit residues: 64.8608 Evaluate side-chains 272 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 245 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 90 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN A 651 ASN B 577 GLN B 651 ASN C 577 GLN E 300 ASN F 352 HIS ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.134165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100399 restraints weight = 28008.258| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.08 r_work: 0.3066 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 20439 Z= 0.273 Angle : 0.787 22.070 27954 Z= 0.361 Chirality : 0.054 0.818 3330 Planarity : 0.004 0.055 3399 Dihedral : 8.479 68.607 4449 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.97 % Allowed : 15.06 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.17), residues: 2301 helix: 0.91 (0.26), residues: 432 sheet: 0.12 (0.19), residues: 720 loop : -0.73 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 178 TYR 0.015 0.002 TYR M 97 PHE 0.020 0.002 PHE M 78 TRP 0.014 0.002 TRP F 427 HIS 0.009 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.27 (20304) covalent geometry : angle 0.69139 / 0.34 (27591) SS BOND : bond 0.00346 / 0.20 ( 42) SS BOND : angle 1.40473 / 0.90 ( 84) hydrogen bonds : bond 0.04444 / 2.88 ( 684) hydrogen bonds : angle 5.05218 / 3.55 ( 1998) link_ALPHA1-2 : bond 0.00138 / 0.07 ( 6) link_ALPHA1-2 : angle 2.12574 / 1.27 ( 18) link_ALPHA1-3 : bond 0.02939 / 1.67 ( 6) link_ALPHA1-3 : angle 4.63190 / 2.84 ( 18) link_ALPHA1-6 : bond 0.00743 / 0.37 ( 3) link_ALPHA1-6 : angle 1.26798 / 0.71 ( 9) link_BETA1-4 : bond 0.00674 / 0.42 ( 21) link_BETA1-4 : angle 2.43414 / 1.63 ( 63) link_NAG-ASN : bond 0.00547 / 0.35 ( 57) link_NAG-ASN : angle 4.27527 / 2.86 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 254 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 ARG cc_start: 0.8143 (mtm180) cc_final: 0.7918 (mtm180) REVERT: B 625 ASN cc_start: 0.7477 (m-40) cc_final: 0.6827 (t0) REVERT: E 47 ASP cc_start: 0.8578 (p0) cc_final: 0.8328 (p0) REVERT: E 97 LYS cc_start: 0.8403 (mtmm) cc_final: 0.8079 (mmmm) REVERT: E 102 GLU cc_start: 0.7938 (mp0) cc_final: 0.7436 (mp0) REVERT: E 104 MET cc_start: 0.8621 (ttt) cc_final: 0.8282 (ttt) REVERT: E 114 GLN cc_start: 0.7975 (tt0) cc_final: 0.7262 (mm-40) REVERT: E 167 ASP cc_start: 0.8784 (m-30) cc_final: 0.8368 (m-30) REVERT: E 189 LYS cc_start: 0.7271 (mmtm) cc_final: 0.6612 (mmmt) REVERT: E 246 GLN cc_start: 0.6228 (tp-100) cc_final: 0.5670 (tt0) REVERT: E 289 ASN cc_start: 0.9043 (p0) cc_final: 0.8798 (p0) REVERT: F 97 LYS cc_start: 0.8339 (mtmm) cc_final: 0.8068 (mmmm) REVERT: F 102 GLU cc_start: 0.7960 (mp0) cc_final: 0.7567 (mp0) REVERT: F 114 GLN cc_start: 0.7957 (tt0) cc_final: 0.7238 (mm-40) REVERT: F 189 LYS cc_start: 0.7356 (mmtm) cc_final: 0.6644 (mmmt) REVERT: F 246 GLN cc_start: 0.6220 (tp-100) cc_final: 0.5856 (tt0) REVERT: F 492 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: G 92 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7749 (mm-30) REVERT: G 97 LYS cc_start: 0.8332 (mppt) cc_final: 0.7943 (mmmm) REVERT: G 102 GLU cc_start: 0.8002 (mp0) cc_final: 0.7529 (mp0) REVERT: G 114 GLN cc_start: 0.7939 (tt0) cc_final: 0.7390 (mt0) REVERT: G 189 LYS cc_start: 0.7390 (mmtm) cc_final: 0.6773 (mmmt) REVERT: G 246 GLN cc_start: 0.6049 (tp-100) cc_final: 0.5627 (tt0) REVERT: G 467 THR cc_start: 0.7707 (OUTLIER) cc_final: 0.7164 (p) REVERT: H 38 ARG cc_start: 0.8770 (ttp-170) cc_final: 0.8569 (ttp-170) REVERT: K 90 GLN cc_start: 0.8250 (tt0) cc_final: 0.8033 (tt0) REVERT: L 39 LYS cc_start: 0.7744 (mtpp) cc_final: 0.7264 (mtmt) REVERT: L 90 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: N 54 ARG cc_start: 0.8579 (ttm110) cc_final: 0.8158 (ttp-110) REVERT: N 90 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8196 (tt0) outliers start: 62 outliers final: 46 residues processed: 294 average time/residue: 0.1481 time to fit residues: 67.1663 Evaluate side-chains 272 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 658 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 88 ASN Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 90 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 199 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 211 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 651 ASN C 650 GLN K 27 GLN L 90 GLN N 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102331 restraints weight = 27833.024| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.06 r_work: 0.3091 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20439 Z= 0.144 Angle : 0.651 14.338 27954 Z= 0.297 Chirality : 0.049 0.597 3330 Planarity : 0.003 0.048 3399 Dihedral : 7.720 61.333 4449 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.17 % Favored : 95.70 % Rotamer: Outliers : 2.54 % Allowed : 17.12 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.17), residues: 2301 helix: 1.27 (0.27), residues: 414 sheet: 0.12 (0.19), residues: 720 loop : -0.75 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 178 TYR 0.012 0.001 TYR F 173 PHE 0.013 0.001 PHE G 53 TRP 0.010 0.001 TRP M 103 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (20304) covalent geometry : angle 0.57055 / 0.28 (27591) SS BOND : bond 0.00338 / 0.23 ( 42) SS BOND : angle 1.07573 / 0.68 ( 84) hydrogen bonds : bond 0.03450 / 2.24 ( 684) hydrogen bonds : angle 4.74992 / 3.33 ( 1998) link_ALPHA1-2 : bond 0.00425 / 0.22 ( 6) link_ALPHA1-2 : angle 1.87421 / 1.10 ( 18) link_ALPHA1-3 : bond 0.02741 / 1.56 ( 6) link_ALPHA1-3 : angle 4.03809 / 2.44 ( 18) link_ALPHA1-6 : bond 0.00832 / 0.41 ( 3) link_ALPHA1-6 : angle 1.48591 / 0.79 ( 9) link_BETA1-4 : bond 0.00688 / 0.41 ( 21) link_BETA1-4 : angle 2.19830 / 1.46 ( 63) link_NAG-ASN : bond 0.00584 / 0.37 ( 57) link_NAG-ASN : angle 3.49994 / 2.36 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 235 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 ARG cc_start: 0.8096 (mtm180) cc_final: 0.7895 (mtm-85) REVERT: B 625 ASN cc_start: 0.7526 (m-40) cc_final: 0.6796 (t0) REVERT: E 47 ASP cc_start: 0.8601 (p0) cc_final: 0.8345 (p0) REVERT: E 97 LYS cc_start: 0.8352 (mtmm) cc_final: 0.8005 (mmmm) REVERT: E 102 GLU cc_start: 0.7799 (mp0) cc_final: 0.7299 (mp0) REVERT: E 104 MET cc_start: 0.8593 (ttt) cc_final: 0.8318 (ttt) REVERT: E 114 GLN cc_start: 0.7775 (tt0) cc_final: 0.7078 (mm-40) REVERT: E 123 THR cc_start: 0.9101 (m) cc_final: 0.8771 (p) REVERT: E 189 LYS cc_start: 0.7220 (mmtm) cc_final: 0.6564 (mmmt) REVERT: E 273 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.6836 (mtt90) REVERT: E 289 ASN cc_start: 0.8980 (p0) cc_final: 0.8630 (p0) REVERT: F 46 LYS cc_start: 0.8328 (mmtp) cc_final: 0.8046 (mttt) REVERT: F 97 LYS cc_start: 0.8293 (mtmm) cc_final: 0.7997 (mmmm) REVERT: F 102 GLU cc_start: 0.7868 (mp0) cc_final: 0.7452 (mp0) REVERT: F 111 LEU cc_start: 0.8137 (mp) cc_final: 0.7907 (tt) REVERT: F 114 GLN cc_start: 0.7842 (tt0) cc_final: 0.7123 (mm-40) REVERT: F 189 LYS cc_start: 0.7303 (mmtm) cc_final: 0.6594 (mmmt) REVERT: F 246 GLN cc_start: 0.5969 (tp-100) cc_final: 0.5610 (tt0) REVERT: F 492 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: G 46 LYS cc_start: 0.8405 (mmmm) cc_final: 0.8188 (mtmt) REVERT: G 47 ASP cc_start: 0.8610 (m-30) cc_final: 0.8401 (m-30) REVERT: G 92 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7747 (mm-30) REVERT: G 97 LYS cc_start: 0.8264 (mppt) cc_final: 0.7825 (mmmm) REVERT: G 102 GLU cc_start: 0.7944 (mp0) cc_final: 0.7461 (mp0) REVERT: G 111 LEU cc_start: 0.8155 (mp) cc_final: 0.7882 (tt) REVERT: G 114 GLN cc_start: 0.7778 (tt0) cc_final: 0.7063 (mm-40) REVERT: G 189 LYS cc_start: 0.7331 (mmtm) cc_final: 0.6595 (mmmt) REVERT: G 246 GLN cc_start: 0.5880 (tp-100) cc_final: 0.5462 (tt0) REVERT: G 289 ASN cc_start: 0.9018 (p0) cc_final: 0.8683 (p0) REVERT: G 475 MET cc_start: 0.7980 (mmm) cc_final: 0.7716 (mmt) REVERT: K 90 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: L 39 LYS cc_start: 0.7684 (mtpp) cc_final: 0.7197 (mtmt) REVERT: L 90 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: N 54 ARG cc_start: 0.8542 (ttm110) cc_final: 0.8245 (ttp-110) REVERT: N 90 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.8006 (tt0) outliers start: 53 outliers final: 33 residues processed: 267 average time/residue: 0.1451 time to fit residues: 59.5630 Evaluate side-chains 264 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain N residue 90 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 91 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 127 optimal weight: 0.6980 chunk 205 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 650 GLN K 27 GLN ** K 27DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN N 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.100952 restraints weight = 27723.262| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.03 r_work: 0.3072 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20439 Z= 0.176 Angle : 0.665 12.124 27954 Z= 0.305 Chirality : 0.049 0.529 3330 Planarity : 0.003 0.046 3399 Dihedral : 7.533 60.086 4449 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.35 % Favored : 95.52 % Rotamer: Outliers : 3.26 % Allowed : 17.03 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2301 helix: 1.23 (0.27), residues: 414 sheet: 0.09 (0.19), residues: 720 loop : -0.77 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 178 TYR 0.013 0.001 TYR B 638 PHE 0.013 0.001 PHE F 53 TRP 0.009 0.001 TRP E 338 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (20304) covalent geometry : angle 0.58793 / 0.29 (27591) SS BOND : bond 0.00235 / 0.14 ( 42) SS BOND : angle 1.14246 / 0.71 ( 84) hydrogen bonds : bond 0.03603 / 2.35 ( 684) hydrogen bonds : angle 4.75114 / 3.33 ( 1998) link_ALPHA1-2 : bond 0.00287 / 0.15 ( 6) link_ALPHA1-2 : angle 1.92637 / 1.14 ( 18) link_ALPHA1-3 : bond 0.02790 / 1.58 ( 6) link_ALPHA1-3 : angle 4.33764 / 2.64 ( 18) link_ALPHA1-6 : bond 0.00884 / 0.44 ( 3) link_ALPHA1-6 : angle 1.49566 / 0.80 ( 9) link_BETA1-4 : bond 0.00655 / 0.40 ( 21) link_BETA1-4 : angle 2.15935 / 1.44 ( 63) link_NAG-ASN : bond 0.00523 / 0.32 ( 57) link_NAG-ASN : angle 3.42240 / 2.28 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 228 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 625 ASN cc_start: 0.7525 (m-40) cc_final: 0.6796 (t0) REVERT: E 47 ASP cc_start: 0.8600 (p0) cc_final: 0.8347 (p0) REVERT: E 97 LYS cc_start: 0.8356 (mtmm) cc_final: 0.7997 (mmmm) REVERT: E 102 GLU cc_start: 0.7803 (mp0) cc_final: 0.7292 (mp0) REVERT: E 104 MET cc_start: 0.8563 (ttt) cc_final: 0.8292 (ttt) REVERT: E 114 GLN cc_start: 0.7812 (tt0) cc_final: 0.7101 (mm-40) REVERT: E 123 THR cc_start: 0.9106 (m) cc_final: 0.8771 (p) REVERT: E 189 LYS cc_start: 0.7208 (mmtm) cc_final: 0.6555 (mmmt) REVERT: E 273 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.6883 (mtt90) REVERT: E 289 ASN cc_start: 0.8994 (p0) cc_final: 0.8737 (p0) REVERT: F 46 LYS cc_start: 0.8336 (mmtp) cc_final: 0.8043 (mttt) REVERT: F 97 LYS cc_start: 0.8295 (mtmm) cc_final: 0.7988 (mmmm) REVERT: F 100 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8419 (mtm) REVERT: F 102 GLU cc_start: 0.7915 (mp0) cc_final: 0.7516 (mp0) REVERT: F 114 GLN cc_start: 0.7830 (tt0) cc_final: 0.7112 (mm-40) REVERT: F 189 LYS cc_start: 0.7288 (mmtm) cc_final: 0.6565 (mmmt) REVERT: F 246 GLN cc_start: 0.5930 (tp-100) cc_final: 0.5569 (tt0) REVERT: F 492 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: G 46 LYS cc_start: 0.8413 (mmmm) cc_final: 0.8184 (mtmt) REVERT: G 92 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7773 (mm-30) REVERT: G 97 LYS cc_start: 0.8262 (mppt) cc_final: 0.7838 (mmmm) REVERT: G 102 GLU cc_start: 0.7921 (mp0) cc_final: 0.7443 (mp0) REVERT: G 111 LEU cc_start: 0.8155 (mp) cc_final: 0.7893 (tt) REVERT: G 114 GLN cc_start: 0.7794 (tt0) cc_final: 0.7066 (mm-40) REVERT: G 189 LYS cc_start: 0.7339 (mmtm) cc_final: 0.6699 (mmmt) REVERT: G 273 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7133 (mtt90) REVERT: G 289 ASN cc_start: 0.9032 (p0) cc_final: 0.8702 (p0) REVERT: K 90 GLN cc_start: 0.8169 (tt0) cc_final: 0.7894 (tt0) REVERT: L 39 LYS cc_start: 0.7749 (mtpp) cc_final: 0.7247 (mtmt) REVERT: L 79 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7313 (mt-10) REVERT: N 54 ARG cc_start: 0.8579 (ttm110) cc_final: 0.8289 (ttp-110) outliers start: 68 outliers final: 48 residues processed: 278 average time/residue: 0.1434 time to fit residues: 60.6487 Evaluate side-chains 269 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 217 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 90 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 86 optimal weight: 0.0980 chunk 140 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 0.0270 chunk 212 optimal weight: 3.9990 chunk 0 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 198 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 411 ASN K 27 GLN L 27DHIS L 90 GLN N 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.137401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.104302 restraints weight = 27496.260| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.04 r_work: 0.3119 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20439 Z= 0.107 Angle : 0.611 10.397 27954 Z= 0.280 Chirality : 0.046 0.477 3330 Planarity : 0.003 0.042 3399 Dihedral : 7.101 59.986 4449 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.26 % Favored : 95.61 % Rotamer: Outliers : 2.54 % Allowed : 17.94 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2301 helix: 1.70 (0.27), residues: 393 sheet: 0.12 (0.19), residues: 720 loop : -0.68 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 178 TYR 0.011 0.001 TYR B 638 PHE 0.012 0.001 PHE F 53 TRP 0.010 0.001 TRP E 338 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (20304) covalent geometry : angle 0.54037 / 0.26 (27591) SS BOND : bond 0.00194 / 0.12 ( 42) SS BOND : angle 1.02941 / 0.67 ( 84) hydrogen bonds : bond 0.03010 / 1.96 ( 684) hydrogen bonds : angle 4.56586 / 3.20 ( 1998) link_ALPHA1-2 : bond 0.00475 / 0.25 ( 6) link_ALPHA1-2 : angle 1.73683 / 1.02 ( 18) link_ALPHA1-3 : bond 0.02695 / 1.52 ( 6) link_ALPHA1-3 : angle 4.27952 / 2.60 ( 18) link_ALPHA1-6 : bond 0.00978 / 0.49 ( 3) link_ALPHA1-6 : angle 1.72897 / 0.89 ( 9) link_BETA1-4 : bond 0.00705 / 0.42 ( 21) link_BETA1-4 : angle 1.95218 / 1.31 ( 63) link_NAG-ASN : bond 0.00527 / 0.32 ( 57) link_NAG-ASN : angle 3.09978 / 2.07 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 224 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 528 SER cc_start: 0.8857 (OUTLIER) cc_final: 0.8591 (t) REVERT: B 625 ASN cc_start: 0.7526 (m-40) cc_final: 0.6764 (t0) REVERT: B 648 GLU cc_start: 0.7687 (tp30) cc_final: 0.7449 (pt0) REVERT: E 47 ASP cc_start: 0.8574 (p0) cc_final: 0.8304 (p0) REVERT: E 97 LYS cc_start: 0.8323 (mtmm) cc_final: 0.7974 (mmmm) REVERT: E 102 GLU cc_start: 0.7751 (mp0) cc_final: 0.7238 (mp0) REVERT: E 104 MET cc_start: 0.8619 (ttt) cc_final: 0.8268 (ttt) REVERT: E 114 GLN cc_start: 0.7737 (tt0) cc_final: 0.7030 (mm-40) REVERT: E 123 THR cc_start: 0.9098 (m) cc_final: 0.8763 (p) REVERT: E 142 MET cc_start: 0.6286 (ttp) cc_final: 0.6005 (tpp) REVERT: E 189 LYS cc_start: 0.7236 (mmtm) cc_final: 0.6575 (mmmt) REVERT: E 289 ASN cc_start: 0.8944 (p0) cc_final: 0.8586 (p0) REVERT: E 475 MET cc_start: 0.7688 (mmm) cc_final: 0.7396 (mmp) REVERT: F 46 LYS cc_start: 0.8365 (mmtp) cc_final: 0.7935 (mttt) REVERT: F 97 LYS cc_start: 0.8261 (mtmm) cc_final: 0.7951 (mmmm) REVERT: F 100 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8247 (mtm) REVERT: F 102 GLU cc_start: 0.7829 (mp0) cc_final: 0.7394 (mp0) REVERT: F 114 GLN cc_start: 0.7735 (tt0) cc_final: 0.7013 (mm-40) REVERT: F 189 LYS cc_start: 0.7325 (mmtm) cc_final: 0.6601 (mmmt) REVERT: F 246 GLN cc_start: 0.5835 (tp-100) cc_final: 0.5491 (tt0) REVERT: F 492 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: F 504 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6845 (mmt180) REVERT: G 46 LYS cc_start: 0.8372 (mmmm) cc_final: 0.8150 (mtmt) REVERT: G 92 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7688 (mm-30) REVERT: G 97 LYS cc_start: 0.8268 (mppt) cc_final: 0.7860 (mmmm) REVERT: G 102 GLU cc_start: 0.7921 (mp0) cc_final: 0.7454 (mp0) REVERT: G 114 GLN cc_start: 0.7683 (tt0) cc_final: 0.7056 (mm-40) REVERT: G 189 LYS cc_start: 0.7312 (mmtm) cc_final: 0.6674 (mmmt) REVERT: G 246 GLN cc_start: 0.5815 (tp-100) cc_final: 0.5592 (tp-100) REVERT: G 273 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7161 (mtt90) REVERT: G 289 ASN cc_start: 0.8979 (p0) cc_final: 0.8638 (p0) REVERT: K 4 MET cc_start: 0.8793 (mmm) cc_final: 0.8572 (mmm) REVERT: K 90 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: L 39 LYS cc_start: 0.7730 (mtpp) cc_final: 0.7226 (mtmt) REVERT: L 79 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7276 (mt-10) REVERT: L 90 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.6718 (tt0) REVERT: M 16 GLU cc_start: 0.6584 (pt0) cc_final: 0.5909 (pm20) REVERT: N 22 SER cc_start: 0.8497 (m) cc_final: 0.8243 (t) REVERT: N 54 ARG cc_start: 0.8567 (ttm110) cc_final: 0.8294 (ttp-110) REVERT: N 79 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7411 (mt-10) outliers start: 53 outliers final: 33 residues processed: 262 average time/residue: 0.1560 time to fit residues: 62.2247 Evaluate side-chains 246 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 504 ARG Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 90 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 204 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 116 optimal weight: 0.0270 chunk 45 optimal weight: 0.4980 chunk 183 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.103692 restraints weight = 27538.483| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.01 r_work: 0.3118 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20439 Z= 0.119 Angle : 0.629 21.935 27954 Z= 0.284 Chirality : 0.047 0.453 3330 Planarity : 0.003 0.047 3399 Dihedral : 6.861 58.987 4449 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.13 % Favored : 95.74 % Rotamer: Outliers : 2.73 % Allowed : 17.79 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.17), residues: 2301 helix: 1.72 (0.27), residues: 393 sheet: 0.15 (0.19), residues: 720 loop : -0.65 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 444 TYR 0.010 0.001 TYR B 638 PHE 0.012 0.001 PHE F 53 TRP 0.020 0.001 TRP A 631 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (20304) covalent geometry : angle 0.54125 / 0.26 (27591) SS BOND : bond 0.00144 / 0.09 ( 42) SS BOND : angle 0.96974 / 0.62 ( 84) hydrogen bonds : bond 0.03049 / 1.99 ( 684) hydrogen bonds : angle 4.51906 / 3.17 ( 1998) link_ALPHA1-2 : bond 0.00423 / 0.22 ( 6) link_ALPHA1-2 : angle 1.75872 / 1.04 ( 18) link_ALPHA1-3 : bond 0.02663 / 1.50 ( 6) link_ALPHA1-3 : angle 4.43470 / 2.71 ( 18) link_ALPHA1-6 : bond 0.01025 / 0.51 ( 3) link_ALPHA1-6 : angle 1.70458 / 0.88 ( 9) link_BETA1-4 : bond 0.00705 / 0.42 ( 21) link_BETA1-4 : angle 1.89387 / 1.28 ( 63) link_NAG-ASN : bond 0.00647 / 0.34 ( 57) link_NAG-ASN : angle 3.62371 / 2.42 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 528 SER cc_start: 0.8862 (m) cc_final: 0.8589 (t) REVERT: B 625 ASN cc_start: 0.7496 (m-40) cc_final: 0.6764 (t0) REVERT: E 47 ASP cc_start: 0.8574 (p0) cc_final: 0.8297 (p0) REVERT: E 97 LYS cc_start: 0.8311 (mtmm) cc_final: 0.7987 (mmmm) REVERT: E 102 GLU cc_start: 0.7776 (mp0) cc_final: 0.7280 (mp0) REVERT: E 104 MET cc_start: 0.8633 (ttt) cc_final: 0.8269 (ttt) REVERT: E 114 GLN cc_start: 0.7734 (tt0) cc_final: 0.6984 (mm-40) REVERT: E 142 MET cc_start: 0.6300 (ttp) cc_final: 0.6051 (tpp) REVERT: E 189 LYS cc_start: 0.7257 (mmtm) cc_final: 0.6599 (mmmt) REVERT: E 289 ASN cc_start: 0.8960 (p0) cc_final: 0.8597 (p0) REVERT: E 475 MET cc_start: 0.7715 (mmm) cc_final: 0.7482 (mmp) REVERT: F 97 LYS cc_start: 0.8280 (mtmm) cc_final: 0.7960 (mmmm) REVERT: F 100 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8276 (mtm) REVERT: F 102 GLU cc_start: 0.7844 (mp0) cc_final: 0.7396 (mp0) REVERT: F 114 GLN cc_start: 0.7754 (tt0) cc_final: 0.7019 (mm-40) REVERT: F 189 LYS cc_start: 0.7306 (mmtm) cc_final: 0.6602 (mmmt) REVERT: F 246 GLN cc_start: 0.5849 (tp-100) cc_final: 0.5510 (tt0) REVERT: F 492 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: F 504 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6852 (mmt180) REVERT: G 46 LYS cc_start: 0.8371 (mmmm) cc_final: 0.8137 (mtmt) REVERT: G 92 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7715 (mm-30) REVERT: G 97 LYS cc_start: 0.8270 (mppt) cc_final: 0.7862 (mmmm) REVERT: G 102 GLU cc_start: 0.7942 (mp0) cc_final: 0.7488 (mp0) REVERT: G 114 GLN cc_start: 0.7698 (tt0) cc_final: 0.7069 (mm-40) REVERT: G 189 LYS cc_start: 0.7324 (mmtm) cc_final: 0.6694 (mmmt) REVERT: G 273 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7179 (mtt90) REVERT: G 289 ASN cc_start: 0.8994 (p0) cc_final: 0.8645 (p0) REVERT: G 300 ASN cc_start: 0.8474 (p0) cc_final: 0.7422 (p0) REVERT: K 90 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: L 39 LYS cc_start: 0.7726 (mtpp) cc_final: 0.7221 (mtmt) REVERT: L 79 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7284 (mt-10) REVERT: L 90 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6677 (tt0) REVERT: M 16 GLU cc_start: 0.6598 (pt0) cc_final: 0.6212 (pm20) REVERT: N 22 SER cc_start: 0.8489 (m) cc_final: 0.8250 (t) REVERT: N 54 ARG cc_start: 0.8578 (ttm110) cc_final: 0.8324 (ttp-110) REVERT: N 79 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7536 (mt-10) REVERT: N 90 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6159 (tt0) outliers start: 57 outliers final: 43 residues processed: 262 average time/residue: 0.1405 time to fit residues: 57.1607 Evaluate side-chains 266 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 504 ARG Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 90 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 40 optimal weight: 3.9990 chunk 213 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 158 optimal weight: 0.0470 chunk 38 optimal weight: 8.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 27 GLN L 90 GLN N 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.101798 restraints weight = 27712.131| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.05 r_work: 0.3093 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20439 Z= 0.149 Angle : 0.647 20.774 27954 Z= 0.293 Chirality : 0.048 0.445 3330 Planarity : 0.003 0.048 3399 Dihedral : 6.793 59.408 4449 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.26 % Favored : 95.61 % Rotamer: Outliers : 2.73 % Allowed : 18.37 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.17), residues: 2301 helix: 1.37 (0.27), residues: 414 sheet: 0.11 (0.19), residues: 726 loop : -0.78 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 444 TYR 0.009 0.001 TYR J 97 PHE 0.013 0.001 PHE F 53 TRP 0.015 0.001 TRP E 427 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (20304) covalent geometry : angle 0.56028 / 0.27 (27591) SS BOND : bond 0.00190 / 0.11 ( 42) SS BOND : angle 1.01642 / 0.65 ( 84) hydrogen bonds : bond 0.03326 / 2.18 ( 684) hydrogen bonds : angle 4.52798 / 3.18 ( 1998) link_ALPHA1-2 : bond 0.00310 / 0.16 ( 6) link_ALPHA1-2 : angle 1.86324 / 1.11 ( 18) link_ALPHA1-3 : bond 0.02667 / 1.50 ( 6) link_ALPHA1-3 : angle 4.58961 / 2.79 ( 18) link_ALPHA1-6 : bond 0.01013 / 0.51 ( 3) link_ALPHA1-6 : angle 1.60633 / 0.84 ( 9) link_BETA1-4 : bond 0.00683 / 0.41 ( 21) link_BETA1-4 : angle 1.95274 / 1.32 ( 63) link_NAG-ASN : bond 0.00606 / 0.32 ( 57) link_NAG-ASN : angle 3.61213 / 2.41 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 226 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 622 ILE cc_start: 0.7893 (tt) cc_final: 0.7646 (tt) REVERT: B 528 SER cc_start: 0.8853 (m) cc_final: 0.8591 (t) REVERT: B 625 ASN cc_start: 0.7560 (m-40) cc_final: 0.6810 (t0) REVERT: E 47 ASP cc_start: 0.8603 (p0) cc_final: 0.8334 (p0) REVERT: E 97 LYS cc_start: 0.8328 (mtmm) cc_final: 0.7992 (mmmm) REVERT: E 102 GLU cc_start: 0.7830 (mp0) cc_final: 0.7329 (mp0) REVERT: E 104 MET cc_start: 0.8598 (ttt) cc_final: 0.8212 (ttt) REVERT: E 114 GLN cc_start: 0.7736 (tt0) cc_final: 0.7050 (mm-40) REVERT: E 142 MET cc_start: 0.6324 (ttp) cc_final: 0.6064 (tpp) REVERT: E 189 LYS cc_start: 0.7205 (mmtm) cc_final: 0.6542 (mmmt) REVERT: E 273 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.6891 (mtt90) REVERT: E 396 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7195 (pt) REVERT: F 97 LYS cc_start: 0.8273 (mtmm) cc_final: 0.7943 (mmmm) REVERT: F 100 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8383 (mtm) REVERT: F 102 GLU cc_start: 0.7891 (mp0) cc_final: 0.7475 (mp0) REVERT: F 114 GLN cc_start: 0.7781 (tt0) cc_final: 0.7044 (mm-40) REVERT: F 189 LYS cc_start: 0.7269 (mmtm) cc_final: 0.6569 (mmmt) REVERT: F 246 GLN cc_start: 0.5859 (tp-100) cc_final: 0.5513 (tt0) REVERT: F 273 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.6902 (mtt90) REVERT: F 419 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7795 (mtp85) REVERT: F 492 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: F 504 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6879 (mmt180) REVERT: G 46 LYS cc_start: 0.8381 (mmmm) cc_final: 0.8077 (mtmt) REVERT: G 92 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7772 (mm-30) REVERT: G 97 LYS cc_start: 0.8287 (mppt) cc_final: 0.7880 (mmmm) REVERT: G 102 GLU cc_start: 0.7958 (mp0) cc_final: 0.7489 (mp0) REVERT: G 111 LEU cc_start: 0.8164 (mp) cc_final: 0.7908 (tt) REVERT: G 114 GLN cc_start: 0.7804 (tt0) cc_final: 0.7096 (mm-40) REVERT: G 189 LYS cc_start: 0.7324 (mmtm) cc_final: 0.6680 (mmmt) REVERT: G 273 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7150 (mtt90) REVERT: G 289 ASN cc_start: 0.9017 (p0) cc_final: 0.8682 (p0) REVERT: K 79 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7560 (mt-10) REVERT: K 90 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: L 39 LYS cc_start: 0.7749 (mtpp) cc_final: 0.7237 (mtmt) REVERT: L 79 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7273 (mt-10) REVERT: L 90 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: M 16 GLU cc_start: 0.6726 (pt0) cc_final: 0.5788 (pm20) REVERT: N 22 SER cc_start: 0.8482 (m) cc_final: 0.8262 (t) REVERT: N 54 ARG cc_start: 0.8599 (ttm110) cc_final: 0.8349 (ttp-110) REVERT: N 79 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7556 (mt-10) REVERT: N 90 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7761 (tt0) outliers start: 57 outliers final: 42 residues processed: 264 average time/residue: 0.1565 time to fit residues: 63.0204 Evaluate side-chains 270 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 218 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 273 ARG Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 504 ARG Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 90 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 103 optimal weight: 0.0970 chunk 140 optimal weight: 6.9990 chunk 208 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 27 GLN L 6 GLN L 90 GLN N 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103784 restraints weight = 27482.167| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.02 r_work: 0.3111 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20439 Z= 0.113 Angle : 0.628 20.277 27954 Z= 0.283 Chirality : 0.047 0.429 3330 Planarity : 0.003 0.043 3399 Dihedral : 6.588 58.926 4449 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.35 % Favored : 95.48 % Rotamer: Outliers : 2.59 % Allowed : 18.71 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.18), residues: 2301 helix: 1.72 (0.27), residues: 393 sheet: 0.17 (0.19), residues: 741 loop : -0.68 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 178 TYR 0.009 0.001 TYR B 638 PHE 0.012 0.001 PHE F 53 TRP 0.012 0.001 TRP A 631 HIS 0.006 0.001 HIS N 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (20304) covalent geometry : angle 0.54601 / 0.26 (27591) SS BOND : bond 0.00218 / 0.15 ( 42) SS BOND : angle 0.92855 / 0.59 ( 84) hydrogen bonds : bond 0.03058 / 2.00 ( 684) hydrogen bonds : angle 4.41711 / 3.10 ( 1998) link_ALPHA1-2 : bond 0.00433 / 0.23 ( 6) link_ALPHA1-2 : angle 1.74675 / 1.03 ( 18) link_ALPHA1-3 : bond 0.02590 / 1.46 ( 6) link_ALPHA1-3 : angle 4.51975 / 2.75 ( 18) link_ALPHA1-6 : bond 0.01034 / 0.52 ( 3) link_ALPHA1-6 : angle 1.70729 / 0.88 ( 9) link_BETA1-4 : bond 0.00708 / 0.43 ( 21) link_BETA1-4 : angle 1.84424 / 1.25 ( 63) link_NAG-ASN : bond 0.00577 / 0.31 ( 57) link_NAG-ASN : angle 3.47297 / 2.32 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 227 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 622 ILE cc_start: 0.7857 (tt) cc_final: 0.7612 (tt) REVERT: B 528 SER cc_start: 0.8820 (OUTLIER) cc_final: 0.8575 (t) REVERT: B 625 ASN cc_start: 0.7604 (m-40) cc_final: 0.6812 (t0) REVERT: E 47 ASP cc_start: 0.8580 (p0) cc_final: 0.8308 (p0) REVERT: E 97 LYS cc_start: 0.8310 (mtmm) cc_final: 0.7978 (mmmm) REVERT: E 102 GLU cc_start: 0.7804 (mp0) cc_final: 0.7297 (mp0) REVERT: E 104 MET cc_start: 0.8613 (ttt) cc_final: 0.8254 (ttt) REVERT: E 114 GLN cc_start: 0.7693 (tt0) cc_final: 0.6963 (mm-40) REVERT: E 142 MET cc_start: 0.6368 (ttp) cc_final: 0.6094 (tpp) REVERT: E 189 LYS cc_start: 0.7218 (mmtm) cc_final: 0.6554 (mmmt) REVERT: E 475 MET cc_start: 0.7598 (mmm) cc_final: 0.7286 (mmp) REVERT: F 97 LYS cc_start: 0.8280 (mtmm) cc_final: 0.7951 (mmmm) REVERT: F 100 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8304 (mtm) REVERT: F 102 GLU cc_start: 0.7839 (mp0) cc_final: 0.7420 (mp0) REVERT: F 114 GLN cc_start: 0.7743 (tt0) cc_final: 0.7008 (mm-40) REVERT: F 189 LYS cc_start: 0.7251 (mmtm) cc_final: 0.6559 (mmmt) REVERT: F 246 GLN cc_start: 0.5860 (tp-100) cc_final: 0.5526 (tt0) REVERT: F 273 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.6898 (mtt90) REVERT: F 492 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: F 504 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6846 (mmt180) REVERT: G 46 LYS cc_start: 0.8378 (mmmm) cc_final: 0.8069 (mtmt) REVERT: G 92 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7736 (mm-30) REVERT: G 97 LYS cc_start: 0.8295 (mppt) cc_final: 0.7888 (mmmm) REVERT: G 102 GLU cc_start: 0.7924 (mp0) cc_final: 0.7453 (mp0) REVERT: G 114 GLN cc_start: 0.7713 (tt0) cc_final: 0.7093 (mm-40) REVERT: G 189 LYS cc_start: 0.7289 (mmtm) cc_final: 0.6654 (mmmt) REVERT: G 273 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7163 (mtt90) REVERT: G 289 ASN cc_start: 0.8994 (p0) cc_final: 0.8653 (p0) REVERT: K 4 MET cc_start: 0.8789 (mmm) cc_final: 0.7661 (mmm) REVERT: K 79 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7519 (mt-10) REVERT: K 90 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: L 39 LYS cc_start: 0.7731 (mtpp) cc_final: 0.7239 (mtmt) REVERT: L 79 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7239 (mt-10) REVERT: M 16 GLU cc_start: 0.6604 (pt0) cc_final: 0.5680 (pm20) REVERT: N 22 SER cc_start: 0.8481 (m) cc_final: 0.8266 (t) REVERT: N 54 ARG cc_start: 0.8601 (ttm110) cc_final: 0.8356 (ttp-110) REVERT: N 79 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7510 (mt-10) outliers start: 54 outliers final: 43 residues processed: 260 average time/residue: 0.1449 time to fit residues: 57.5906 Evaluate side-chains 263 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 273 ARG Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 504 ARG Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 208 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 177 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 27 GLN L 90 GLN M 1 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.134989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.101924 restraints weight = 27679.120| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.05 r_work: 0.3087 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20439 Z= 0.144 Angle : 0.645 20.001 27954 Z= 0.292 Chirality : 0.047 0.427 3330 Planarity : 0.003 0.056 3399 Dihedral : 6.604 59.843 4449 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.48 % Favored : 95.39 % Rotamer: Outliers : 2.49 % Allowed : 19.09 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2301 helix: 1.38 (0.27), residues: 414 sheet: 0.15 (0.19), residues: 744 loop : -0.76 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 444 TYR 0.008 0.001 TYR F 173 PHE 0.013 0.001 PHE F 53 TRP 0.013 0.001 TRP E 427 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (20304) covalent geometry : angle 0.56345 / 0.27 (27591) SS BOND : bond 0.00210 / 0.13 ( 42) SS BOND : angle 1.02507 / 0.65 ( 84) hydrogen bonds : bond 0.03286 / 2.15 ( 684) hydrogen bonds : angle 4.47985 / 3.15 ( 1998) link_ALPHA1-2 : bond 0.00303 / 0.16 ( 6) link_ALPHA1-2 : angle 1.84558 / 1.10 ( 18) link_ALPHA1-3 : bond 0.02661 / 1.51 ( 6) link_ALPHA1-3 : angle 4.67207 / 2.83 ( 18) link_ALPHA1-6 : bond 0.01097 / 0.55 ( 3) link_ALPHA1-6 : angle 1.66671 / 0.87 ( 9) link_BETA1-4 : bond 0.00688 / 0.41 ( 21) link_BETA1-4 : angle 1.89488 / 1.29 ( 63) link_NAG-ASN : bond 0.00549 / 0.29 ( 57) link_NAG-ASN : angle 3.49798 / 2.33 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 219 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 622 ILE cc_start: 0.7872 (tt) cc_final: 0.7618 (tt) REVERT: B 528 SER cc_start: 0.8788 (m) cc_final: 0.8552 (t) REVERT: B 625 ASN cc_start: 0.7594 (m-40) cc_final: 0.6809 (t0) REVERT: E 47 ASP cc_start: 0.8590 (p0) cc_final: 0.8315 (p0) REVERT: E 97 LYS cc_start: 0.8318 (mtmm) cc_final: 0.7986 (mmmm) REVERT: E 102 GLU cc_start: 0.7819 (mp0) cc_final: 0.7318 (mp0) REVERT: E 104 MET cc_start: 0.8595 (ttt) cc_final: 0.8213 (ttt) REVERT: E 114 GLN cc_start: 0.7736 (tt0) cc_final: 0.7006 (mm-40) REVERT: E 142 MET cc_start: 0.6415 (ttp) cc_final: 0.6140 (tpp) REVERT: E 189 LYS cc_start: 0.7198 (mmtm) cc_final: 0.6513 (mmmt) REVERT: E 475 MET cc_start: 0.7658 (mmm) cc_final: 0.7377 (mmp) REVERT: F 97 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7913 (mmmm) REVERT: F 102 GLU cc_start: 0.7910 (mp0) cc_final: 0.7494 (mp0) REVERT: F 114 GLN cc_start: 0.7802 (tt0) cc_final: 0.7058 (mm-40) REVERT: F 189 LYS cc_start: 0.7240 (mmtm) cc_final: 0.6539 (mmmt) REVERT: F 246 GLN cc_start: 0.5831 (tp-100) cc_final: 0.5499 (tt0) REVERT: F 273 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.6888 (mtt90) REVERT: F 419 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7789 (mtp85) REVERT: F 492 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: F 504 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.6860 (mmt180) REVERT: G 46 LYS cc_start: 0.8367 (mmmm) cc_final: 0.8061 (mtmt) REVERT: G 92 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7756 (mm-30) REVERT: G 97 LYS cc_start: 0.8303 (mppt) cc_final: 0.7896 (mmmm) REVERT: G 102 GLU cc_start: 0.7946 (mp0) cc_final: 0.7472 (mp0) REVERT: G 114 GLN cc_start: 0.7744 (tt0) cc_final: 0.7067 (mm-40) REVERT: G 189 LYS cc_start: 0.7242 (mmtm) cc_final: 0.6614 (mmmt) REVERT: G 273 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7157 (mtt90) REVERT: G 289 ASN cc_start: 0.9038 (p0) cc_final: 0.8689 (p0) REVERT: K 79 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7528 (mt-10) REVERT: K 90 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: L 79 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7330 (mt-10) REVERT: M 16 GLU cc_start: 0.6649 (pt0) cc_final: 0.5669 (pm20) REVERT: N 22 SER cc_start: 0.8501 (m) cc_final: 0.8292 (t) REVERT: N 54 ARG cc_start: 0.8619 (ttm110) cc_final: 0.8366 (ttp-110) REVERT: N 79 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7519 (mt-10) outliers start: 52 outliers final: 43 residues processed: 255 average time/residue: 0.1535 time to fit residues: 59.6651 Evaluate side-chains 262 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 273 ARG Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain F residue 504 ARG Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 57 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 35 optimal weight: 0.0570 chunk 222 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 132 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 1 GLN K 27 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.135132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102370 restraints weight = 27661.514| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.02 r_work: 0.3099 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20439 Z= 0.131 Angle : 0.631 19.792 27954 Z= 0.285 Chirality : 0.047 0.426 3330 Planarity : 0.003 0.041 3399 Dihedral : 6.493 59.370 4449 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.35 % Favored : 95.48 % Rotamer: Outliers : 2.35 % Allowed : 19.33 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.17), residues: 2301 helix: 1.43 (0.27), residues: 411 sheet: 0.18 (0.19), residues: 744 loop : -0.75 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 178 TYR 0.009 0.001 TYR L 87 PHE 0.012 0.001 PHE F 53 TRP 0.012 0.001 TRP E 427 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (20304) covalent geometry : angle 0.55040 / 0.27 (27591) SS BOND : bond 0.00193 / 0.12 ( 42) SS BOND : angle 0.92908 / 0.59 ( 84) hydrogen bonds : bond 0.03157 / 2.07 ( 684) hydrogen bonds : angle 4.43628 / 3.12 ( 1998) link_ALPHA1-2 : bond 0.00371 / 0.20 ( 6) link_ALPHA1-2 : angle 1.77620 / 1.05 ( 18) link_ALPHA1-3 : bond 0.02557 / 1.44 ( 6) link_ALPHA1-3 : angle 4.58943 / 2.78 ( 18) link_ALPHA1-6 : bond 0.01046 / 0.52 ( 3) link_ALPHA1-6 : angle 1.65537 / 0.85 ( 9) link_BETA1-4 : bond 0.00688 / 0.41 ( 21) link_BETA1-4 : angle 1.85481 / 1.26 ( 63) link_NAG-ASN : bond 0.00556 / 0.29 ( 57) link_NAG-ASN : angle 3.43045 / 2.29 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4083.35 seconds wall clock time: 70 minutes 59.47 seconds (4259.47 seconds total)