Starting phenix.real_space_refine on Sat Jul 4 14:55:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ly9_23589/07_2026/7ly9_23589.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ly9_23589/07_2026/7ly9_23589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ly9_23589/07_2026/7ly9_23589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ly9_23589/07_2026/7ly9_23589.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ly9_23589/07_2026/7ly9_23589.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ly9_23589/07_2026/7ly9_23589.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ly9_23589/07_2026/7ly9_23589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ly9_23589/07_2026/7ly9_23589.cif" } resolution = 3.91 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= 0.010 sd= 0.061 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 126 5.16 5 C 13467 2.51 5 N 3572 2.21 5 O 4299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21464 Number of models: 1 Model: "" Number of chains: 35 Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "H" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1023 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3449 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "B" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "F" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 899 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Chain: "D" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3440 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Chain: "E" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "J" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 924 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Chain: "K" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3442 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Chain: "A" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "M" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 767 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "N" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 912 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain breaks: 1 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 chiralities: 2 Chain: "P" 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 chiralities: 2 Chain: "Q" 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 chiralities: 7 Chain: "R" 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 chiralities: 4 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 7 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 7 Chain: "G" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 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 chiralities: 1 Chain: "F" 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 chiralities: 2 Chain: "D" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen chiralities: 16 Chain: "I" 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 chiralities: 1 Chain: "J" 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 chiralities: 2 Chain: "K" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Chain: "M" 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 chiralities: 1 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.48, per 1000 atoms: 0.21 Number of scatterers: 21464 At special positions: 0 Unit cell: (149.07, 139.205, 146.877, 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 126 16.00 O 4299 8.00 N 3572 7.00 C 13467 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 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=2.04 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.04 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.04 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS N 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 598 " - pdb=" SG CYS N 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA Q 3 " - " MAN Q 7 " " MAN Q 4 " - " MAN Q 5 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 7 " " MAN U 4 " - " MAN U 5 " " BMA Z 3 " - " MAN Z 7 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-6 " BMA Q 3 " - " MAN Q 4 " " MAN Q 4 " - " MAN Q 6 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 6 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 6 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " NAG-ASN " NAG C 301 " - " ASN C 72 " " NAG D 601 " - " ASN D 130 " " NAG D 602 " - " ASN D 156 " " NAG D 603 " - " ASN D 230 " " NAG D 604 " - " ASN D 241 " " NAG D 605 " - " ASN D 301 " " NAG D 606 " - " ASN D 362 " " NAG D 607 " - " ASN D 442 " " NAG D 608 " - " ASN D 448 " " NAG D 609 " - " ASN D 393 " " NAG D 610 " - " ASN D 197 " " NAG D 611 " - " ASN D 88 " " NAG D 612 " - " ASN D 234 " " NAG D 613 " - " ASN D 502 " " NAG D 614 " - " ASN D 461 " " NAG D 615 " - " ASN D 356 " " NAG D 616 " - " ASN D 386 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 601 " - " ASN G 230 " " NAG G 602 " - " ASN G 241 " " NAG G 603 " - " ASN G 301 " " NAG G 604 " - " ASN G 356 " " NAG G 605 " - " ASN G 362 " " NAG G 606 " - " ASN G 386 " " NAG G 607 " - " ASN G 442 " " NAG G 608 " - " ASN G 448 " " NAG G 609 " - " ASN G 502 " " NAG G 610 " - " ASN G 393 " " NAG G 611 " - " ASN G 197 " " NAG G 612 " - " ASN G 130 " " NAG G 613 " - " ASN G 156 " " NAG G 614 " - " ASN G 234 " " NAG G 615 " - " ASN G 88 " " NAG I 301 " - " ASN I 72 " " NAG J 701 " - " ASN J 637 " " NAG J 702 " - " ASN J 611 " " NAG K 601 " - " ASN K 130 " " NAG K 602 " - " ASN K 156 " " NAG K 603 " - " ASN K 230 " " NAG K 604 " - " ASN K 234 " " NAG K 605 " - " ASN K 241 " " NAG K 606 " - " ASN K 301 " " NAG K 607 " - " ASN K 362 " " NAG K 608 " - " ASN K 386 " " NAG K 609 " - " ASN K 442 " " NAG K 610 " - " ASN K 448 " " NAG K 611 " - " ASN K 393 " " NAG K 612 " - " ASN K 197 " " NAG K 613 " - " ASN K 502 " " NAG K 614 " - " ASN K 88 " " NAG M 301 " - " ASN M 72 " " NAG N 701 " - " ASN N 611 " " NAG N 702 " - " ASN N 637 " " NAG O 1 " - " ASN G 289 " " NAG P 1 " - " ASN G 332 " " NAG Q 1 " - " ASN G 276 " " NAG R 1 " - " ASN G 262 " " NAG S 1 " - " ASN D 289 " " NAG T 1 " - " ASN D 332 " " NAG U 1 " - " ASN D 276 " " NAG V 1 " - " ASN D 262 " " NAG W 1 " - " ASN K 262 " " NAG X 1 " - " ASN K 289 " " NAG Y 1 " - " ASN K 332 " " NAG Z 1 " - " ASN K 276 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 901.7 milliseconds 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4696 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 58 sheets defined 17.7% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'L' and resid 27 through 31 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.888A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 98 Processing helix chain 'G' and resid 99 through 116 Processing helix chain 'G' and resid 335 through 356 removed outlier: 3.716A pdb=" N GLU G 351 " --> pdb=" O GLU G 347 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE G 353 " --> pdb=" O LEU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.650A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 392 removed outlier: 4.198A pdb=" N PHE G 392 " --> pdb=" O ASP G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.743A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'F' and resid 516 through 524 removed outlier: 3.806A pdb=" N PHE F 522 " --> pdb=" O VAL F 518 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU F 523 " --> pdb=" O PHE F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 536 removed outlier: 3.994A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 6.262A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU F 587 " --> pdb=" O ILE F 583 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.643A pdb=" N ILE F 622 " --> pdb=" O THR F 618 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 637 removed outlier: 3.666A pdb=" N ARG F 633 " --> pdb=" O MET F 629 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN F 637 " --> pdb=" O ARG F 633 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 657 removed outlier: 3.633A pdb=" N VAL F 648 " --> pdb=" O LYS F 644 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.322A pdb=" N ASP D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 356 removed outlier: 3.553A pdb=" N GLN D 343 " --> pdb=" O GLU D 339 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 351 " --> pdb=" O GLU D 347 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 481 removed outlier: 4.088A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 4.190A pdb=" N THR E 87 " --> pdb=" O SER E 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 515 through 523 removed outlier: 4.353A pdb=" N PHE J 519 " --> pdb=" O LEU J 515 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE J 522 " --> pdb=" O VAL J 518 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU J 523 " --> pdb=" O PHE J 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 536 removed outlier: 3.518A pdb=" N SER J 534 " --> pdb=" O MET J 530 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN J 535 " --> pdb=" O GLY J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 595 removed outlier: 6.396A pdb=" N GLN J 575 " --> pdb=" O TRP J 571 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 626 Processing helix chain 'J' and resid 627 through 636 removed outlier: 3.520A pdb=" N TRP J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP J 632 " --> pdb=" O TRP J 628 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG J 633 " --> pdb=" O MET J 629 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 660 removed outlier: 3.508A pdb=" N VAL J 648 " --> pdb=" O LYS J 644 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS J 658 " --> pdb=" O GLU J 654 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 117 removed outlier: 3.538A pdb=" N LYS K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 356 removed outlier: 3.688A pdb=" N LYS K 348 " --> pdb=" O ARG K 344 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU K 351 " --> pdb=" O GLU K 347 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N HIS K 352 " --> pdb=" O LYS K 348 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE K 353 " --> pdb=" O LEU K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 388 through 392 removed outlier: 4.147A pdb=" N PHE K 392 " --> pdb=" O ASP K 389 " (cutoff:3.500A) Processing helix chain 'K' and resid 475 through 481 removed outlier: 4.161A pdb=" N TRP K 479 " --> pdb=" O MET K 475 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER K 481 " --> pdb=" O ASP K 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 83 through 87 removed outlier: 4.041A pdb=" N THR A 87 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 517 through 523 removed outlier: 3.828A pdb=" N LEU N 523 " --> pdb=" O PHE N 519 " (cutoff:3.500A) Processing helix chain 'N' and resid 529 through 536 Processing helix chain 'N' and resid 569 through 596 removed outlier: 3.560A pdb=" N PHE N 573 " --> pdb=" O GLY N 569 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN N 575 " --> pdb=" O TRP N 571 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU N 576 " --> pdb=" O GLY N 572 " (cutoff:3.500A) Processing helix chain 'N' and resid 627 through 636 removed outlier: 3.717A pdb=" N TRP N 631 " --> pdb=" O THR N 627 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP N 632 " --> pdb=" O TRP N 628 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG N 633 " --> pdb=" O MET N 629 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU N 634 " --> pdb=" O GLN N 630 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 659 removed outlier: 3.615A pdb=" N GLN N 650 " --> pdb=" O LEU N 646 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE N 651 " --> pdb=" O GLU N 647 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AA2, first strand: chain 'L' and resid 22 through 24 removed outlier: 3.632A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.540A pdb=" N ASP L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL L 90 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL L 97 " --> pdb=" O VAL L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.191A pdb=" N SER H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP H 72 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR H 79 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 17 through 18 Processing sheet with id=AA6, first strand: chain 'H' and resid 45 through 50 removed outlier: 6.844A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 99 through 100 Processing sheet with id=AA8, first strand: chain 'G' and resid 35 through 40 removed outlier: 3.586A pdb=" N THR G 499 " --> pdb=" O TRP G 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.508A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.612A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE G 53 " --> pdb=" O CYS G 218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 91 through 92 removed outlier: 3.538A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 169 through 177 removed outlier: 4.281A pdb=" N SER G 158 " --> pdb=" O ASN G 130 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN G 130 " --> pdb=" O SER G 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 200 through 203 removed outlier: 6.674A pdb=" N VAL G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N TYR G 435 " --> pdb=" O VAL G 200 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 259 through 261 removed outlier: 4.825A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS G 445 " --> pdb=" O CYS G 296 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 271 through 274 Processing sheet with id=AB7, first strand: chain 'G' and resid 304 through 312 removed outlier: 3.657A pdb=" N ILE G 309 " --> pdb=" O GLN G 315 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 332 through 334 Processing sheet with id=AB9, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.861A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE G 383 " --> pdb=" O PHE G 376 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR G 384 " --> pdb=" O ARG G 419 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG G 419 " --> pdb=" O TYR G 384 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.579A pdb=" N GLU B 23 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL B 18 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B 82 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 20 " --> pdb=" O MET B 80 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR B 70 " --> pdb=" O TYR B 79 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 57 through 58 removed outlier: 6.507A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TRP B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 33 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS B 35 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.532A pdb=" N CYS C 23 " --> pdb=" O TYR C 71 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AC5, first strand: chain 'C' and resid 53 through 54 removed outlier: 7.039A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE C 87 " --> pdb=" O TYR C 36 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 494 through 498 Processing sheet with id=AC7, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.664A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AC9, first strand: chain 'D' and resid 91 through 94 removed outlier: 3.510A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE D 93 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY D 237 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 130 through 131 removed outlier: 3.970A pdb=" N ASN D 130 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER D 158 " --> pdb=" O ASN D 130 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG D 170 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AD3, first strand: chain 'D' and resid 394 through 395 removed outlier: 3.500A pdb=" N PHE D 361 " --> pdb=" O LYS D 394 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 292 " --> pdb=" O ILE D 449 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER D 334 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR D 295 " --> pdb=" O ASN D 332 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN D 332 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR D 297 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N HIS D 330 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG D 419 " --> pdb=" O TYR D 384 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 384 " --> pdb=" O ARG D 419 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE D 376 " --> pdb=" O PHE D 383 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 259 through 261 removed outlier: 3.998A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 271 through 274 Processing sheet with id=AD6, first strand: chain 'D' and resid 444 through 445 Processing sheet with id=AD7, first strand: chain 'D' and resid 305 through 312 removed outlier: 3.773A pdb=" N LYS D 305 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.998A pdb=" N THR E 110 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR E 90 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP E 37 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TRP E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 18 through 24 removed outlier: 3.857A pdb=" N VAL E 18 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU E 82 " --> pdb=" O VAL E 18 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.988A pdb=" N GLN I 24 " --> pdb=" O THR I 5 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 18 through 22 removed outlier: 3.882A pdb=" N SER I 63 " --> pdb=" O THR I 74 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 53 through 54 removed outlier: 7.060A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 53 through 54 removed outlier: 7.060A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR I 86 " --> pdb=" O THR I 102 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR I 102 " --> pdb=" O TYR I 86 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 35 through 36 Processing sheet with id=AE6, first strand: chain 'K' and resid 39 through 40 Processing sheet with id=AE7, first strand: chain 'K' and resid 45 through 47 Processing sheet with id=AE8, first strand: chain 'K' and resid 75 through 76 removed outlier: 3.900A pdb=" N VAL K 75 " --> pdb=" O CYS K 54 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE K 53 " --> pdb=" O CYS K 218 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 91 through 94 removed outlier: 4.173A pdb=" N PHE K 93 " --> pdb=" O GLY K 237 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY K 237 " --> pdb=" O PHE K 93 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 130 through 131 removed outlier: 3.883A pdb=" N ASN K 130 " --> pdb=" O SER K 158 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER K 158 " --> pdb=" O ASN K 130 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA K 161 " --> pdb=" O ARG K 170 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG K 170 " --> pdb=" O ALA K 161 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 181 through 183 Processing sheet with id=AF3, first strand: chain 'K' and resid 200 through 203 removed outlier: 6.691A pdb=" N VAL K 200 " --> pdb=" O ALA K 433 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR K 435 " --> pdb=" O VAL K 200 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET K 434 " --> pdb=" O ILE K 424 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 259 through 261 removed outlier: 4.784A pdb=" N LEU K 260 " --> pdb=" O THR K 450 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS K 445 " --> pdb=" O CYS K 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL K 292 " --> pdb=" O ILE K 449 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 271 through 273 removed outlier: 6.829A pdb=" N ILE K 360 " --> pdb=" O PHE K 468 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS K 394 " --> pdb=" O PHE K 361 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 304 through 308 Processing sheet with id=AF7, first strand: chain 'K' and resid 332 through 334 Processing sheet with id=AF8, first strand: chain 'K' and resid 377 through 378 removed outlier: 4.423A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS K 421 " --> pdb=" O PHE K 382 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR K 384 " --> pdb=" O ARG K 419 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG K 419 " --> pdb=" O TYR K 384 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 4 through 6 removed outlier: 4.103A pdb=" N VAL A 18 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 82 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 77 " --> pdb=" O HIS A 71A" (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP A 81 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 10 through 11 removed outlier: 3.503A pdb=" N ALA A 10 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 110 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 107 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 90 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 10 through 11 removed outlier: 3.503A pdb=" N ALA A 10 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 110 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 107 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 90 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 94 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 4 through 6 removed outlier: 3.525A pdb=" N ILE M 21 " --> pdb=" O LEU M 73 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TRP M 67 " --> pdb=" O GLU M 70 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN M 72 " --> pdb=" O ARG M 65 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG M 65 " --> pdb=" O ASN M 72 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER M 63 " --> pdb=" O THR M 74 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 53 through 54 removed outlier: 6.949A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1527 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: 4.33 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3520 1.32 - 1.45: 6391 1.45 - 1.58: 11851 1.58 - 1.70: 2 1.70 - 1.83: 166 Bond restraints: 21930 Sorted by residual: bond pdb=" OH TYS H 100A" pdb=" S TYS H 100A" ideal model delta sigma weight residual 1.679 1.564 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" CA TYR C 91 " pdb=" C TYR C 91 " ideal model delta sigma weight residual 1.523 1.587 -0.064 1.34e-02 5.57e+03 2.29e+01 bond pdb=" OH TYS H 100C" pdb=" S TYS H 100C" ideal model delta sigma weight residual 1.679 1.600 0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" N THR D 358 " pdb=" CA THR D 358 " ideal model delta sigma weight residual 1.456 1.501 -0.045 1.22e-02 6.72e+03 1.37e+01 bond pdb=" N GLU G 190 " pdb=" CA GLU G 190 " ideal model delta sigma weight residual 1.455 1.499 -0.044 1.25e-02 6.40e+03 1.23e+01 ... (remaining 21925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 28989 2.06 - 4.12: 667 4.12 - 6.18: 119 6.18 - 8.24: 7 8.24 - 10.30: 4 Bond angle restraints: 29786 Sorted by residual: angle pdb=" C ASN D 262 " pdb=" CA ASN D 262 " pdb=" CB ASN D 262 " ideal model delta sigma weight residual 115.89 105.59 10.30 1.32e+00 5.74e-01 6.09e+01 angle pdb=" CA TYR C 91 " pdb=" C TYR C 91 " pdb=" O TYR C 91 " ideal model delta sigma weight residual 120.51 111.88 8.63 1.43e+00 4.89e-01 3.64e+01 angle pdb=" CA TYR C 91 " pdb=" C TYR C 91 " pdb=" N GLU C 96 " ideal model delta sigma weight residual 116.84 125.45 -8.61 1.71e+00 3.42e-01 2.54e+01 angle pdb=" CA PRO G 214 " pdb=" C PRO G 214 " pdb=" O PRO G 214 " ideal model delta sigma weight residual 121.36 115.89 5.47 1.13e+00 7.83e-01 2.34e+01 angle pdb=" CA ASN D 262 " pdb=" CB ASN D 262 " pdb=" CG ASN D 262 " ideal model delta sigma weight residual 112.60 117.36 -4.76 1.00e+00 1.00e+00 2.27e+01 ... (remaining 29781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10956 17.95 - 35.90: 1037 35.90 - 53.85: 231 53.85 - 71.80: 26 71.80 - 89.75: 21 Dihedral angle restraints: 12271 sinusoidal: 4968 harmonic: 7303 Sorted by residual: dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual 93.00 166.44 -73.44 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual -86.00 -141.05 55.05 1 1.00e+01 1.00e-02 4.10e+01 dihedral pdb=" CB CYS D 218 " pdb=" SG CYS D 218 " pdb=" SG CYS D 247 " pdb=" CB CYS D 247 " ideal model delta sinusoidal sigma weight residual -86.00 -136.25 50.25 1 1.00e+01 1.00e-02 3.46e+01 ... (remaining 12268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3468 0.134 - 0.267: 58 0.267 - 0.401: 10 0.401 - 0.535: 1 0.535 - 0.669: 1 Chirality restraints: 3538 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN D 262 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CA THR G 209 " pdb=" N THR G 209 " pdb=" C THR G 209 " pdb=" CB THR G 209 " both_signs ideal model delta sigma weight residual False 2.53 2.94 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA LEU D 261 " pdb=" N LEU D 261 " pdb=" C LEU D 261 " pdb=" CB LEU D 261 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 3535 not shown) Planarity restraints: 3752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 262 " 0.041 2.00e-02 2.50e+03 4.13e-02 2.13e+01 pdb=" CG ASN D 262 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN D 262 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN D 262 " -0.062 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 252 " 0.061 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO D 253 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO D 253 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 253 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 208 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C VAL G 208 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL G 208 " 0.023 2.00e-02 2.50e+03 pdb=" N THR G 209 " 0.020 2.00e-02 2.50e+03 ... (remaining 3749 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 232 2.58 - 3.16: 18061 3.16 - 3.74: 29802 3.74 - 4.32: 41891 4.32 - 4.90: 70675 Nonbonded interactions: 160661 Sorted by model distance: nonbonded pdb=" OD2 ASP G 457 " pdb=" OG1 THR G 467 " model vdw 2.003 3.040 nonbonded pdb=" O THR G 209 " pdb=" OG1 THR G 209 " model vdw 2.160 3.040 nonbonded pdb=" O PRO C 8 " pdb=" OG SER C 9 " model vdw 2.222 3.040 nonbonded pdb=" NH2 ARG I 66 " pdb=" O7 NAG U 2 " model vdw 2.233 3.120 nonbonded pdb=" O SER N 612 " pdb=" ND2 ASN N 616 " model vdw 2.245 3.120 ... (remaining 160656 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 1 through 104 or resid 301)) selection = (chain 'I' and (resid 1 through 104 or resid 301)) selection = chain 'M' } ncs_group { reference = (chain 'D' and (resid 33 through 503 or resid 603 through 615)) selection = (chain 'G' and (resid 33 through 397 or resid 410 through 503 or resid 603 throu \ gh 615)) selection = (chain 'K' and (resid 33 through 397 or resid 410 through 613)) } ncs_group { reference = (chain 'F' and resid 516 through 702) selection = (chain 'J' and (resid 516 through 657 or resid 701 through 702)) selection = (chain 'N' and (resid 516 through 657 or resid 701 through 702)) } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'Q' 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 group one per residue 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: 6.340 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 20.410 Find NCS groups from input model: 0.440 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 0.115 22066 Z= 0.250 Angle : 0.739 18.253 30154 Z= 0.373 Chirality : 0.054 0.669 3538 Planarity : 0.003 0.094 3686 Dihedral : 14.361 89.754 7455 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.78 % Favored : 94.18 % Rotamer: Outliers : 0.76 % Allowed : 0.45 % Favored : 98.79 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.18), residues: 2475 helix: 1.78 (0.32), residues: 318 sheet: 0.17 (0.22), residues: 609 loop : -0.71 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 308 TYR 0.028 0.001 TYR C 91 PHE 0.010 0.001 PHE A 73 TRP 0.015 0.001 TRP D 479 HIS 0.003 0.000 HIS K 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.25 (21930) covalent geometry : angle 0.71826 / 0.37 (29786) SS BOND : bond 0.00246 / 0.16 ( 40) SS BOND : angle 1.23470 / 0.79 ( 80) hydrogen bonds : bond 0.29540 / 19.75 ( 579) hydrogen bonds : angle 9.69905 / 6.96 ( 1527) link_ALPHA1-3 : bond 0.00410 / 0.22 ( 7) link_ALPHA1-3 : angle 1.62043 / 0.90 ( 21) link_ALPHA1-6 : bond 0.00392 / 0.21 ( 6) link_ALPHA1-6 : angle 1.64341 / 0.93 ( 18) link_BETA1-4 : bond 0.00316 / 0.19 ( 17) link_BETA1-4 : angle 1.24510 / 0.75 ( 51) link_NAG-ASN : bond 0.00858 / 0.52 ( 66) link_NAG-ASN : angle 2.03077 / 1.48 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.892 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: F 612 SER cc_start: 0.8393 (m) cc_final: 0.8123 (p) REVERT: E 4 LEU cc_start: 0.8323 (tp) cc_final: 0.7916 (tp) REVERT: N 595 MET cc_start: 0.7342 (ptm) cc_final: 0.6997 (ttp) REVERT: N 639 THR cc_start: 0.8111 (p) cc_final: 0.7831 (t) outliers start: 17 outliers final: 4 residues processed: 210 average time/residue: 0.1790 time to fit residues: 55.6120 Evaluate side-chains 102 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 230 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 358 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 0.3980 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 10 ASN H 82AASN ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 ASN B 6 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN F 653 GLN D 105 HIS D 287 HIS D 330 HIS ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 ASN K 377 ASN A 56 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.035824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.028767 restraints weight = 187666.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.029696 restraints weight = 102317.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.030333 restraints weight = 68998.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.030785 restraints weight = 52715.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.031083 restraints weight = 43468.445| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 22066 Z= 0.308 Angle : 0.826 11.226 30154 Z= 0.412 Chirality : 0.049 0.354 3538 Planarity : 0.006 0.103 3686 Dihedral : 5.433 53.883 2744 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.12 % Allowed : 8.68 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.17), residues: 2475 helix: 1.07 (0.28), residues: 341 sheet: -0.12 (0.21), residues: 634 loop : -1.03 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 61 TYR 0.023 0.003 TYR E 99 PHE 0.022 0.002 PHE D 382 TRP 0.022 0.002 TRP N 631 HIS 0.007 0.001 HIS L 95B Details of bonding type rmsd/Z covalent geometry : bond 0.00675 / 0.31 (21930) covalent geometry : angle 0.79531 / 0.41 (29786) SS BOND : bond 0.00505 / 0.32 ( 40) SS BOND : angle 1.70873 / 1.13 ( 80) hydrogen bonds : bond 0.05566 / 3.67 ( 579) hydrogen bonds : angle 6.54040 / 4.65 ( 1527) link_ALPHA1-3 : bond 0.00486 / 0.23 ( 7) link_ALPHA1-3 : angle 2.02784 / 1.12 ( 21) link_ALPHA1-6 : bond 0.00544 / 0.34 ( 6) link_ALPHA1-6 : angle 1.95437 / 1.17 ( 18) link_BETA1-4 : bond 0.00762 / 0.42 ( 17) link_BETA1-4 : angle 1.90396 / 1.09 ( 51) link_NAG-ASN : bond 0.00575 / 0.35 ( 66) link_NAG-ASN : angle 2.42305 / 1.79 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 104 MET cc_start: 0.8993 (ttt) cc_final: 0.8559 (tmm) REVERT: G 302 MET cc_start: 0.8387 (mmp) cc_final: 0.8150 (mmp) REVERT: G 434 MET cc_start: 0.8697 (mtt) cc_final: 0.8445 (mtt) REVERT: D 377 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8749 (t0) REVERT: K 95 MET cc_start: 0.9338 (ppp) cc_final: 0.8932 (ppp) REVERT: K 104 MET cc_start: 0.9638 (ttt) cc_final: 0.9082 (ttt) outliers start: 25 outliers final: 10 residues processed: 116 average time/residue: 0.1419 time to fit residues: 26.6376 Evaluate side-chains 95 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain K residue 475 MET Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain N residue 603 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 134 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN G 203 GLN A 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.036000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.028952 restraints weight = 184878.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.029907 restraints weight = 99833.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.030540 restraints weight = 66787.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.030958 restraints weight = 50934.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.031294 restraints weight = 42641.868| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22066 Z= 0.147 Angle : 0.619 8.889 30154 Z= 0.310 Chirality : 0.045 0.338 3538 Planarity : 0.004 0.043 3686 Dihedral : 4.958 58.609 2740 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.17 % Allowed : 10.84 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.17), residues: 2475 helix: 1.61 (0.29), residues: 335 sheet: -0.03 (0.20), residues: 653 loop : -0.95 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 83 TYR 0.022 0.001 TYR E 27 PHE 0.029 0.001 PHE F 522 TRP 0.014 0.001 TRP B 71D HIS 0.003 0.001 HIS L 95B Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (21930) covalent geometry : angle 0.59359 / 0.30 (29786) SS BOND : bond 0.00419 / 0.26 ( 40) SS BOND : angle 1.21725 / 0.80 ( 80) hydrogen bonds : bond 0.04917 / 3.22 ( 579) hydrogen bonds : angle 5.84428 / 4.17 ( 1527) link_ALPHA1-3 : bond 0.00583 / 0.29 ( 7) link_ALPHA1-3 : angle 1.42075 / 0.79 ( 21) link_ALPHA1-6 : bond 0.00568 / 0.33 ( 6) link_ALPHA1-6 : angle 1.60676 / 0.93 ( 18) link_BETA1-4 : bond 0.00416 / 0.24 ( 17) link_BETA1-4 : angle 1.48709 / 0.83 ( 51) link_NAG-ASN : bond 0.00343 / 0.22 ( 66) link_NAG-ASN : angle 1.91182 / 1.35 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 TYR cc_start: 0.8989 (m-10) cc_final: 0.8786 (m-10) REVERT: G 104 MET cc_start: 0.8971 (ttt) cc_final: 0.8696 (tmt) REVERT: G 302 MET cc_start: 0.8667 (mmp) cc_final: 0.8377 (mmp) REVERT: F 530 MET cc_start: 0.8341 (mmm) cc_final: 0.7013 (mmm) REVERT: F 595 MET cc_start: 0.9218 (ttp) cc_final: 0.8652 (tmm) REVERT: E 80 MET cc_start: 0.9128 (tmm) cc_final: 0.8836 (tmm) REVERT: K 104 MET cc_start: 0.9628 (ttt) cc_final: 0.8984 (tmt) outliers start: 26 outliers final: 13 residues processed: 115 average time/residue: 0.1305 time to fit residues: 25.0537 Evaluate side-chains 97 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain M residue 21 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 4 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 238 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 199 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 616 ASN K 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.033742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.026875 restraints weight = 189501.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.027763 restraints weight = 102385.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.028368 restraints weight = 68807.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.028795 restraints weight = 52490.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.029055 restraints weight = 43361.549| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 22066 Z= 0.292 Angle : 0.754 8.714 30154 Z= 0.375 Chirality : 0.046 0.307 3538 Planarity : 0.004 0.048 3686 Dihedral : 5.282 56.821 2740 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.29 % Allowed : 12.73 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.83 (0.17), residues: 2475 helix: 1.32 (0.28), residues: 345 sheet: -0.29 (0.19), residues: 702 loop : -1.18 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 61 TYR 0.042 0.002 TYR E 99 PHE 0.023 0.002 PHE D 396 TRP 0.022 0.002 TRP G 427 HIS 0.005 0.001 HIS D 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.29 (21930) covalent geometry : angle 0.72440 / 0.37 (29786) SS BOND : bond 0.00400 / 0.26 ( 40) SS BOND : angle 1.65126 / 1.09 ( 80) hydrogen bonds : bond 0.04547 / 2.96 ( 579) hydrogen bonds : angle 5.70481 / 4.04 ( 1527) link_ALPHA1-3 : bond 0.00437 / 0.20 ( 7) link_ALPHA1-3 : angle 1.76012 / 0.98 ( 21) link_ALPHA1-6 : bond 0.00424 / 0.27 ( 6) link_ALPHA1-6 : angle 1.88136 / 1.12 ( 18) link_BETA1-4 : bond 0.00465 / 0.25 ( 17) link_BETA1-4 : angle 1.62671 / 0.91 ( 51) link_NAG-ASN : bond 0.00460 / 0.30 ( 66) link_NAG-ASN : angle 2.29808 / 1.61 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 76 time to evaluate : 0.802 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: G 100 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8853 (mtm) REVERT: G 302 MET cc_start: 0.8539 (mmp) cc_final: 0.8271 (mmp) REVERT: F 595 MET cc_start: 0.9154 (ttp) cc_final: 0.8386 (tmm) REVERT: D 95 MET cc_start: 0.8671 (pmm) cc_final: 0.7836 (pmm) REVERT: D 179 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8692 (pp) REVERT: E 5 LEU cc_start: 0.9105 (tp) cc_final: 0.8880 (pp) REVERT: E 80 MET cc_start: 0.9237 (tmm) cc_final: 0.8954 (tmm) REVERT: K 95 MET cc_start: 0.9394 (ppp) cc_final: 0.8976 (ppp) REVERT: K 104 MET cc_start: 0.9638 (ttt) cc_final: 0.9060 (ttt) REVERT: K 229 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8621 (p0) outliers start: 51 outliers final: 27 residues processed: 122 average time/residue: 0.1117 time to fit residues: 23.2226 Evaluate side-chains 102 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 230 ASN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 229 ASN Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain N residue 603 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 212 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.033309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.026513 restraints weight = 189103.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.027385 restraints weight = 102051.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.027988 restraints weight = 68577.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.028357 restraints weight = 52239.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.028674 restraints weight = 44034.315| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 22066 Z= 0.252 Angle : 0.706 9.144 30154 Z= 0.351 Chirality : 0.045 0.319 3538 Planarity : 0.004 0.045 3686 Dihedral : 5.260 50.935 2740 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.52 % Allowed : 14.17 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.17), residues: 2475 helix: 1.60 (0.29), residues: 327 sheet: -0.50 (0.19), residues: 738 loop : -1.17 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 61 TYR 0.024 0.002 TYR E 27 PHE 0.024 0.002 PHE F 522 TRP 0.020 0.002 TRP B 71D HIS 0.008 0.001 HIS K 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.25 (21930) covalent geometry : angle 0.67459 / 0.34 (29786) SS BOND : bond 0.00507 / 0.35 ( 40) SS BOND : angle 1.88411 / 1.22 ( 80) hydrogen bonds : bond 0.04274 / 2.82 ( 579) hydrogen bonds : angle 5.55392 / 3.93 ( 1527) link_ALPHA1-3 : bond 0.00423 / 0.20 ( 7) link_ALPHA1-3 : angle 1.63152 / 0.91 ( 21) link_ALPHA1-6 : bond 0.00382 / 0.24 ( 6) link_ALPHA1-6 : angle 1.91356 / 1.13 ( 18) link_BETA1-4 : bond 0.00358 / 0.20 ( 17) link_BETA1-4 : angle 1.46774 / 0.82 ( 51) link_NAG-ASN : bond 0.00306 / 0.20 ( 66) link_NAG-ASN : angle 2.20273 / 1.58 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 78 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 101 ASP cc_start: 0.9661 (OUTLIER) cc_final: 0.9067 (p0) REVERT: F 595 MET cc_start: 0.9107 (ttp) cc_final: 0.8350 (tmm) REVERT: D 95 MET cc_start: 0.8672 (pmm) cc_final: 0.7856 (pmm) REVERT: E 4 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8698 (tp) REVERT: E 80 MET cc_start: 0.9260 (tmm) cc_final: 0.8911 (tmm) REVERT: K 95 MET cc_start: 0.9393 (ppp) cc_final: 0.8870 (ppp) REVERT: K 104 MET cc_start: 0.9646 (ttt) cc_final: 0.9088 (ttt) REVERT: K 480 ARG cc_start: 0.9436 (OUTLIER) cc_final: 0.9101 (tpp80) outliers start: 56 outliers final: 36 residues processed: 128 average time/residue: 0.1164 time to fit residues: 25.1444 Evaluate side-chains 110 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 71 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 229 ASN Chi-restraints excluded: chain G residue 230 ASN Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 491 VAL Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain K residue 475 MET Chi-restraints excluded: chain K residue 480 ARG Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 632 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 chunk 171 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 197 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 66 ASN G 478 ASN ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 652 GLN ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.033071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.026321 restraints weight = 190698.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.027190 restraints weight = 102118.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.027774 restraints weight = 68486.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.028218 restraints weight = 52294.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.028508 restraints weight = 42853.864| |-----------------------------------------------------------------------------| r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 22066 Z= 0.224 Angle : 0.679 8.822 30154 Z= 0.336 Chirality : 0.045 0.315 3538 Planarity : 0.004 0.038 3686 Dihedral : 5.189 51.389 2740 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.38 % Allowed : 15.52 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.17), residues: 2475 helix: 1.66 (0.29), residues: 333 sheet: -0.50 (0.19), residues: 736 loop : -1.18 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.023 0.001 TYR E 27 PHE 0.022 0.002 PHE F 522 TRP 0.018 0.001 TRP B 71D HIS 0.004 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 (21930) covalent geometry : angle 0.64824 / 0.33 (29786) SS BOND : bond 0.00450 / 0.29 ( 40) SS BOND : angle 1.73788 / 1.15 ( 80) hydrogen bonds : bond 0.03989 / 2.63 ( 579) hydrogen bonds : angle 5.40072 / 3.83 ( 1527) link_ALPHA1-3 : bond 0.00400 / 0.19 ( 7) link_ALPHA1-3 : angle 1.60496 / 0.90 ( 21) link_ALPHA1-6 : bond 0.00377 / 0.23 ( 6) link_ALPHA1-6 : angle 1.82323 / 1.07 ( 18) link_BETA1-4 : bond 0.00360 / 0.19 ( 17) link_BETA1-4 : angle 1.46472 / 0.82 ( 51) link_NAG-ASN : bond 0.00295 / 0.19 ( 66) link_NAG-ASN : angle 2.15627 / 1.54 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 75 time to evaluate : 0.641 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: H 82 MET cc_start: 0.9134 (mpp) cc_final: 0.8569 (mpp) REVERT: G 100 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8877 (mtm) REVERT: G 297 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8129 (p) REVERT: G 302 MET cc_start: 0.8545 (mmp) cc_final: 0.7974 (mmp) REVERT: F 595 MET cc_start: 0.9089 (ttp) cc_final: 0.8425 (tmm) REVERT: D 95 MET cc_start: 0.8667 (pmm) cc_final: 0.7854 (pmm) REVERT: K 95 MET cc_start: 0.9389 (ppp) cc_final: 0.8193 (ppp) REVERT: K 104 MET cc_start: 0.9622 (ttt) cc_final: 0.9089 (ttt) REVERT: K 229 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8544 (p0) REVERT: K 480 ARG cc_start: 0.9455 (OUTLIER) cc_final: 0.8505 (mtm-85) outliers start: 53 outliers final: 41 residues processed: 124 average time/residue: 0.1192 time to fit residues: 25.0359 Evaluate side-chains 116 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 71 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 229 ASN Chi-restraints excluded: chain G residue 230 ASN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 229 ASN Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain K residue 475 MET Chi-restraints excluded: chain K residue 480 ARG Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 603 ILE Chi-restraints excluded: chain N residue 618 THR Chi-restraints excluded: chain N residue 632 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 47 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 239 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.033165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.026428 restraints weight = 188511.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.027298 restraints weight = 101023.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.027905 restraints weight = 67671.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.028268 restraints weight = 51392.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.028568 restraints weight = 43358.593| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22066 Z= 0.179 Angle : 0.647 9.345 30154 Z= 0.319 Chirality : 0.045 0.323 3538 Planarity : 0.004 0.041 3686 Dihedral : 5.180 68.187 2739 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.43 % Allowed : 16.01 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.17), residues: 2475 helix: 1.76 (0.29), residues: 333 sheet: -0.50 (0.19), residues: 740 loop : -1.13 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.018 0.001 TYR E 27 PHE 0.023 0.001 PHE F 522 TRP 0.034 0.002 TRP D 427 HIS 0.003 0.001 HIS K 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (21930) covalent geometry : angle 0.61905 / 0.31 (29786) SS BOND : bond 0.00505 / 0.31 ( 40) SS BOND : angle 1.52246 / 0.98 ( 80) hydrogen bonds : bond 0.03753 / 2.47 ( 579) hydrogen bonds : angle 5.27471 / 3.74 ( 1527) link_ALPHA1-3 : bond 0.00457 / 0.23 ( 7) link_ALPHA1-3 : angle 1.53394 / 0.86 ( 21) link_ALPHA1-6 : bond 0.00427 / 0.26 ( 6) link_ALPHA1-6 : angle 1.73074 / 1.02 ( 18) link_BETA1-4 : bond 0.00327 / 0.18 ( 17) link_BETA1-4 : angle 1.41369 / 0.79 ( 51) link_NAG-ASN : bond 0.00261 / 0.17 ( 66) link_NAG-ASN : angle 2.03744 / 1.45 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 75 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 82 MET cc_start: 0.9071 (mpp) cc_final: 0.8568 (mpp) REVERT: H 101 ASP cc_start: 0.9687 (OUTLIER) cc_final: 0.8579 (p0) REVERT: G 100 MET cc_start: 0.9163 (mtm) cc_final: 0.8914 (mtm) REVERT: G 104 MET cc_start: 0.8877 (tmm) cc_final: 0.8463 (tmm) REVERT: G 297 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8080 (p) REVERT: G 302 MET cc_start: 0.8565 (mmp) cc_final: 0.7966 (mmp) REVERT: G 467 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8826 (p) REVERT: F 595 MET cc_start: 0.9072 (ttp) cc_final: 0.8442 (tmm) REVERT: F 610 TRP cc_start: 0.8856 (OUTLIER) cc_final: 0.8166 (m100) REVERT: D 95 MET cc_start: 0.8657 (pmm) cc_final: 0.7848 (pmm) REVERT: D 104 MET cc_start: 0.8592 (ttp) cc_final: 0.8351 (ttp) REVERT: E 80 MET cc_start: 0.8916 (tmm) cc_final: 0.8708 (tmm) REVERT: K 95 MET cc_start: 0.9387 (ppp) cc_final: 0.8178 (ppp) REVERT: K 104 MET cc_start: 0.9635 (ttt) cc_final: 0.9096 (ttt) REVERT: K 229 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8541 (p0) REVERT: K 467 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8659 (p) REVERT: K 480 ARG cc_start: 0.9443 (OUTLIER) cc_final: 0.8491 (mtm-85) outliers start: 54 outliers final: 36 residues processed: 126 average time/residue: 0.1211 time to fit residues: 26.2474 Evaluate side-chains 116 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 73 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 229 ASN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 229 ASN Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain K residue 467 THR Chi-restraints excluded: chain K residue 475 MET Chi-restraints excluded: chain K residue 480 ARG Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 618 THR Chi-restraints excluded: chain N residue 632 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 109 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 105 HIS C 6 GLN ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 HIS ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.031940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.025278 restraints weight = 194844.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.026123 restraints weight = 104443.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.026700 restraints weight = 69959.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.027106 restraints weight = 53329.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.027378 restraints weight = 44100.216| |-----------------------------------------------------------------------------| r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 22066 Z= 0.347 Angle : 0.810 9.298 30154 Z= 0.397 Chirality : 0.047 0.284 3538 Planarity : 0.005 0.040 3686 Dihedral : 5.572 68.571 2737 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 2.61 % Allowed : 16.46 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.17), residues: 2475 helix: 1.34 (0.28), residues: 335 sheet: -0.66 (0.19), residues: 767 loop : -1.39 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 61 TYR 0.017 0.002 TYR I 91 PHE 0.021 0.002 PHE D 392 TRP 0.042 0.002 TRP D 427 HIS 0.005 0.001 HIS D 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.35 (21930) covalent geometry : angle 0.77783 / 0.39 (29786) SS BOND : bond 0.00613 / 0.38 ( 40) SS BOND : angle 1.98081 / 1.30 ( 80) hydrogen bonds : bond 0.04355 / 2.86 ( 579) hydrogen bonds : angle 5.62962 / 3.98 ( 1527) link_ALPHA1-3 : bond 0.00427 / 0.20 ( 7) link_ALPHA1-3 : angle 1.89092 / 1.05 ( 21) link_ALPHA1-6 : bond 0.00273 / 0.17 ( 6) link_ALPHA1-6 : angle 2.07746 / 1.24 ( 18) link_BETA1-4 : bond 0.00452 / 0.25 ( 17) link_BETA1-4 : angle 1.65725 / 0.92 ( 51) link_NAG-ASN : bond 0.00487 / 0.30 ( 66) link_NAG-ASN : angle 2.43801 / 1.74 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 70 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 82 MET cc_start: 0.9158 (mpp) cc_final: 0.8631 (mpp) REVERT: G 100 MET cc_start: 0.9152 (mtm) cc_final: 0.8878 (mtm) REVERT: G 104 MET cc_start: 0.8612 (tmm) cc_final: 0.8379 (tmm) REVERT: G 297 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8549 (p) REVERT: G 302 MET cc_start: 0.8509 (mmp) cc_final: 0.7918 (mmp) REVERT: F 595 MET cc_start: 0.9114 (ttp) cc_final: 0.8452 (tmm) REVERT: F 610 TRP cc_start: 0.9011 (OUTLIER) cc_final: 0.8205 (m100) REVERT: D 95 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8415 (ppp) REVERT: J 629 MET cc_start: 0.9004 (tpp) cc_final: 0.8794 (tpp) REVERT: K 95 MET cc_start: 0.9404 (ppp) cc_final: 0.8431 (ppp) REVERT: K 104 MET cc_start: 0.9629 (ttt) cc_final: 0.9047 (ttt) REVERT: K 467 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8595 (p) REVERT: N 626 MET cc_start: 0.8602 (ttm) cc_final: 0.8179 (ttp) outliers start: 58 outliers final: 42 residues processed: 125 average time/residue: 0.1225 time to fit residues: 25.6562 Evaluate side-chains 111 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 65 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 230 ASN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 593 LEU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain K residue 467 THR Chi-restraints excluded: chain K residue 475 MET Chi-restraints excluded: chain K residue 491 VAL Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 618 THR Chi-restraints excluded: chain N residue 632 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 69 optimal weight: 0.6980 chunk 162 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 230 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 236 optimal weight: 0.2980 chunk 109 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 374 HIS E 56 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 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 = 0.2966 r_free = 0.2966 target = 0.033258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.026571 restraints weight = 188555.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.027446 restraints weight = 100176.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.028051 restraints weight = 66920.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.028479 restraints weight = 50812.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.028753 restraints weight = 41785.021| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22066 Z= 0.118 Angle : 0.652 8.796 30154 Z= 0.320 Chirality : 0.045 0.322 3538 Planarity : 0.004 0.046 3686 Dihedral : 5.181 67.751 2737 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.80 % Allowed : 17.18 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.17), residues: 2475 helix: 1.86 (0.29), residues: 333 sheet: -0.47 (0.19), residues: 755 loop : -1.19 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.018 0.001 TYR C 91 PHE 0.024 0.001 PHE F 522 TRP 0.036 0.002 TRP D 427 HIS 0.003 0.001 HIS K 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (21930) covalent geometry : angle 0.62470 / 0.31 (29786) SS BOND : bond 0.00527 / 0.33 ( 40) SS BOND : angle 1.59570 / 1.05 ( 80) hydrogen bonds : bond 0.03577 / 2.35 ( 579) hydrogen bonds : angle 5.13292 / 3.65 ( 1527) link_ALPHA1-3 : bond 0.00524 / 0.28 ( 7) link_ALPHA1-3 : angle 1.48326 / 0.84 ( 21) link_ALPHA1-6 : bond 0.00549 / 0.33 ( 6) link_ALPHA1-6 : angle 1.55628 / 0.90 ( 18) link_BETA1-4 : bond 0.00328 / 0.19 ( 17) link_BETA1-4 : angle 1.38734 / 0.78 ( 51) link_NAG-ASN : bond 0.00341 / 0.21 ( 66) link_NAG-ASN : angle 1.99272 / 1.43 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 72 time to evaluate : 0.615 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: H 82 MET cc_start: 0.9051 (mpp) cc_final: 0.8581 (mpp) REVERT: G 104 MET cc_start: 0.8617 (tmm) cc_final: 0.8409 (tmm) REVERT: G 297 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.8111 (p) REVERT: G 302 MET cc_start: 0.8509 (mmp) cc_final: 0.7878 (mmp) REVERT: F 595 MET cc_start: 0.9085 (ttp) cc_final: 0.8450 (tmm) REVERT: D 95 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7822 (pmm) REVERT: D 104 MET cc_start: 0.8556 (ttp) cc_final: 0.8150 (ttp) REVERT: D 302 MET cc_start: 0.8577 (mmp) cc_final: 0.7572 (mmm) REVERT: K 95 MET cc_start: 0.9293 (ppp) cc_final: 0.8144 (ppp) REVERT: K 104 MET cc_start: 0.9632 (ttt) cc_final: 0.9123 (ttt) REVERT: K 467 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8691 (p) outliers start: 40 outliers final: 31 residues processed: 108 average time/residue: 0.1222 time to fit residues: 22.0723 Evaluate side-chains 105 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 71 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 230 ASN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 TRP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain K residue 467 THR Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 618 THR Chi-restraints excluded: chain N residue 632 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 197 optimal weight: 8.9990 chunk 71 optimal weight: 0.0870 chunk 47 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 82AASN ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.032787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.026120 restraints weight = 189771.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.026976 restraints weight = 101641.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.027572 restraints weight = 68126.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.027989 restraints weight = 51744.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.028267 restraints weight = 42605.311| |-----------------------------------------------------------------------------| r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22066 Z= 0.180 Angle : 0.654 8.573 30154 Z= 0.322 Chirality : 0.045 0.313 3538 Planarity : 0.004 0.043 3686 Dihedral : 5.161 69.960 2737 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.75 % Allowed : 17.23 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.17), residues: 2475 helix: 1.76 (0.29), residues: 339 sheet: -0.43 (0.19), residues: 747 loop : -1.21 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 61 TYR 0.017 0.001 TYR C 91 PHE 0.023 0.001 PHE F 522 TRP 0.039 0.002 TRP D 427 HIS 0.004 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (21930) covalent geometry : angle 0.62661 / 0.32 (29786) SS BOND : bond 0.00463 / 0.29 ( 40) SS BOND : angle 1.61358 / 1.06 ( 80) hydrogen bonds : bond 0.03588 / 2.36 ( 579) hydrogen bonds : angle 5.15974 / 3.66 ( 1527) link_ALPHA1-3 : bond 0.00438 / 0.23 ( 7) link_ALPHA1-3 : angle 1.51118 / 0.85 ( 21) link_ALPHA1-6 : bond 0.00435 / 0.27 ( 6) link_ALPHA1-6 : angle 1.67504 / 0.98 ( 18) link_BETA1-4 : bond 0.00328 / 0.18 ( 17) link_BETA1-4 : angle 1.38141 / 0.77 ( 51) link_NAG-ASN : bond 0.00265 / 0.17 ( 66) link_NAG-ASN : angle 2.02659 / 1.45 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 70 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 82 MET cc_start: 0.9051 (mpp) cc_final: 0.8587 (mpp) REVERT: G 100 MET cc_start: 0.9154 (mtm) cc_final: 0.8899 (mtm) REVERT: G 104 MET cc_start: 0.8671 (tmm) cc_final: 0.8390 (tmm) REVERT: G 297 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8164 (p) REVERT: G 302 MET cc_start: 0.8468 (mmp) cc_final: 0.7889 (mmp) REVERT: F 595 MET cc_start: 0.9066 (ttp) cc_final: 0.8432 (tmm) REVERT: F 610 TRP cc_start: 0.8923 (OUTLIER) cc_final: 0.8723 (m-10) REVERT: D 95 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7827 (pmm) REVERT: D 104 MET cc_start: 0.8603 (ttp) cc_final: 0.8345 (ttp) REVERT: K 95 MET cc_start: 0.9321 (ppp) cc_final: 0.8286 (ppp) REVERT: K 104 MET cc_start: 0.9623 (ttt) cc_final: 0.9086 (ttt) REVERT: K 467 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8687 (p) outliers start: 39 outliers final: 33 residues processed: 107 average time/residue: 0.1226 time to fit residues: 21.8642 Evaluate side-chains 106 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 69 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 230 ASN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 TRP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain K residue 467 THR Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 618 THR Chi-restraints excluded: chain N residue 632 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 26 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 37 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.033439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.026733 restraints weight = 188318.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.027617 restraints weight = 100363.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.028228 restraints weight = 66909.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.028645 restraints weight = 50813.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.028923 restraints weight = 41984.116| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22066 Z= 0.118 Angle : 0.617 8.752 30154 Z= 0.304 Chirality : 0.044 0.326 3538 Planarity : 0.003 0.046 3686 Dihedral : 4.984 69.790 2737 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.66 % Allowed : 17.45 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.17), residues: 2475 helix: 1.88 (0.29), residues: 340 sheet: -0.23 (0.19), residues: 735 loop : -1.18 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 61 TYR 0.014 0.001 TYR C 91 PHE 0.023 0.001 PHE F 522 TRP 0.041 0.001 TRP D 427 HIS 0.003 0.001 HIS K 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (21930) covalent geometry : angle 0.59272 / 0.30 (29786) SS BOND : bond 0.00469 / 0.29 ( 40) SS BOND : angle 1.45742 / 0.96 ( 80) hydrogen bonds : bond 0.03237 / 2.14 ( 579) hydrogen bonds : angle 4.94458 / 3.52 ( 1527) link_ALPHA1-3 : bond 0.00512 / 0.28 ( 7) link_ALPHA1-3 : angle 1.44880 / 0.82 ( 21) link_ALPHA1-6 : bond 0.00529 / 0.31 ( 6) link_ALPHA1-6 : angle 1.56626 / 0.91 ( 18) link_BETA1-4 : bond 0.00319 / 0.18 ( 17) link_BETA1-4 : angle 1.33100 / 0.75 ( 51) link_NAG-ASN : bond 0.00312 / 0.19 ( 66) link_NAG-ASN : angle 1.85207 / 1.33 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2642.61 seconds wall clock time: 47 minutes 4.50 seconds (2824.50 seconds total)