Starting phenix.real_space_refine on Sat Jul 4 15:22:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mep_23801/07_2026/7mep_23801.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mep_23801/07_2026/7mep_23801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mep_23801/07_2026/7mep_23801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mep_23801/07_2026/7mep_23801.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mep_23801/07_2026/7mep_23801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mep_23801/07_2026/7mep_23801.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7mep_23801/07_2026/7mep_23801.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mep_23801/07_2026/7mep_23801.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 128 5.16 5 C 13518 2.51 5 N 3635 2.21 5 O 4355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 21636 Number of models: 1 Model: "" Number of chains: 35 Chain: "G" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "I" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "A" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3477 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 3 Chain: "B" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 985 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "H" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 995 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "J" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain: "M" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "C" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3487 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "E" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 985 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "K" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "N" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "D" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3499 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 20, 'TRANS': 422} Chain breaks: 3 Chain: "F" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 985 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Z" 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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" 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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.91, per 1000 atoms: 0.23 Number of scatterers: 21636 At special positions: 0 Unit cell: (130.81, 126.69, 172.01, 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 128 16.00 O 4355 8.00 N 3635 7.00 C 13518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.06 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.07 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 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 O 3 " - " MAN O 4 " " BMA U 3 " - " MAN U 4 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA U 3 " - " MAN U 5 " " BMA Y 3 " - " MAN Y 5 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 276 " " NAG A 703 " - " ASN A 386 " " NAG A 704 " - " ASN A 363 " " NAG A 705 " - " ASN A 234 " " NAG A 706 " - " ASN A 197 " " NAG A 707 " - " ASN A 133 " " NAG A 708 " - " ASN A 88 " " NAG A 709 " - " ASN A 241 " " NAG A 710 " - " ASN A 289 " " NAG A 711 " - " ASN A 339 " " NAG A 712 " - " ASN A 355 " " NAG A 713 " - " ASN A 392 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 701 " - " ASN C 448 " " NAG C 702 " - " ASN C 160 " " NAG C 703 " - " ASN C 276 " " NAG C 704 " - " ASN C 386 " " NAG C 705 " - " ASN C 363 " " NAG C 706 " - " ASN C 234 " " NAG C 707 " - " ASN C 197 " " NAG C 708 " - " ASN C 133 " " NAG C 709 " - " ASN C 301 " " NAG C 710 " - " ASN C 88 " " NAG C 711 " - " ASN C 241 " " NAG C 712 " - " ASN C 289 " " NAG C 713 " - " ASN C 339 " " NAG C 714 " - " ASN C 355 " " NAG C 715 " - " ASN C 392 " " NAG D 701 " - " ASN D 160 " " NAG D 702 " - " ASN D 276 " " NAG D 703 " - " ASN D 295 " " NAG D 704 " - " ASN D 386 " " NAG D 705 " - " ASN D 363 " " NAG D 706 " - " ASN D 234 " " NAG D 707 " - " ASN D 197 " " NAG D 708 " - " ASN D 133 " " NAG D 709 " - " ASN D 88 " " NAG D 710 " - " ASN D 241 " " NAG D 711 " - " ASN D 289 " " NAG D 712 " - " ASN D 339 " " NAG D 713 " - " ASN D 355 " " NAG D 714 " - " ASN D 392 " " NAG E 701 " - " ASN E 637 " " NAG E 702 " - " ASN E 618 " " NAG E 703 " - " ASN E 611 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 448 " " NAG Q 1 " - " ASN A 295 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 301 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN C 295 " " NAG W 1 " - " ASN C 156 " " NAG X 1 " - " ASN C 332 " " NAG Y 1 " - " ASN D 262 " " NAG Z 1 " - " ASN D 448 " " NAG a 1 " - " ASN D 156 " " NAG b 1 " - " ASN D 301 " " NAG c 1 " - " ASN D 332 " Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 847.9 milliseconds 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4806 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 49 sheets defined 21.3% alpha, 45.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 60 through 65 removed outlier: 4.448A pdb=" N SER I 65 " --> pdb=" O PRO I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.099A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.833A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.600A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.416A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 535 through 541 removed outlier: 5.869A pdb=" N THR B 538 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL B 539 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.838A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 657 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.931A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.084A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 65 removed outlier: 5.403A pdb=" N SER M 65 " --> pdb=" O SER M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.156A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.889A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.976A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.407A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 removed outlier: 3.524A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 596 Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.769A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 657 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.728A pdb=" N VAL K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 65 removed outlier: 5.320A pdb=" N SER N 65 " --> pdb=" O SER N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.518A pdb=" N THR N 87 " --> pdb=" O ALA N 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 73 Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.122A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 354 removed outlier: 4.005A pdb=" N VAL D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 535 through 541 removed outlier: 5.813A pdb=" N THR F 538 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL F 539 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.747A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 658 Processing sheet with id=AA1, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.491A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AA4, first strand: chain 'I' and resid 57 through 59 removed outlier: 3.828A pdb=" N GLY I 44 " --> pdb=" O THR I 40 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TRP I 35 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 57 through 59 removed outlier: 3.828A pdb=" N GLY I 44 " --> pdb=" O THR I 40 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TRP I 35 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.396A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB2, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.515A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.413A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.751A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.849A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.125A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 10.849A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.751A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.841A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.517A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC1, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.590A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.590A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AC4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.623A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'M' and resid 57 through 59 removed outlier: 4.845A pdb=" N GLY M 44 " --> pdb=" O THR M 40 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR M 40 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR M 50 " --> pdb=" O TRP M 35 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TRP M 35 " --> pdb=" O TYR M 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 57 through 59 removed outlier: 4.845A pdb=" N GLY M 44 " --> pdb=" O THR M 40 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR M 40 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR M 50 " --> pdb=" O TRP M 35 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TRP M 35 " --> pdb=" O TYR M 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.916A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AD1, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.332A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AD3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AD4, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.569A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 393 through 395 removed outlier: 6.276A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 10.276A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.123A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.718A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.956A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.718A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.123A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.276A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.523A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AD9, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.903A pdb=" N ALA K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.903A pdb=" N ALA K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'N' and resid 57 through 59 removed outlier: 4.068A pdb=" N GLY N 44 " --> pdb=" O THR N 40 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR N 50 " --> pdb=" O TRP N 35 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TRP N 35 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 57 through 59 removed outlier: 4.068A pdb=" N GLY N 44 " --> pdb=" O THR N 40 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR N 50 " --> pdb=" O TRP N 35 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TRP N 35 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.345A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AE7, first strand: chain 'D' and resid 75 through 76 removed outlier: 4.074A pdb=" N VAL D 75 " --> pdb=" O CYS D 54 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AE9, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AF1, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.523A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 394 through 395 removed outlier: 6.259A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.667A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.997A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.667A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.659A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) 917 hydrogen bonds defined for protein. 2370 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: 4.93 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5042 1.32 - 1.46: 6975 1.46 - 1.59: 9820 1.59 - 1.73: 86 1.73 - 1.87: 157 Bond restraints: 22080 Sorted by residual: bond pdb=" NE ARG C 504 " pdb=" CZ ARG C 504 " ideal model delta sigma weight residual 1.326 1.414 -0.088 1.10e-02 8.26e+03 6.37e+01 bond pdb=" NE ARG K 3 " pdb=" CZ ARG K 3 " ideal model delta sigma weight residual 1.326 1.405 -0.079 1.10e-02 8.26e+03 5.11e+01 bond pdb=" CG GLN K 6 " pdb=" CD GLN K 6 " ideal model delta sigma weight residual 1.516 1.353 0.163 2.50e-02 1.60e+03 4.23e+01 bond pdb=" NE ARG J 3 " pdb=" CZ ARG J 3 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.07e+01 bond pdb=" NE1 TRP I 96 " pdb=" CE2 TRP I 96 " ideal model delta sigma weight residual 1.370 1.303 0.067 1.10e-02 8.26e+03 3.71e+01 ... (remaining 22075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 26499 2.64 - 5.28: 3102 5.28 - 7.92: 370 7.92 - 10.56: 30 10.56 - 13.20: 1 Bond angle restraints: 30002 Sorted by residual: angle pdb=" N ASP B 659 " pdb=" CA ASP B 659 " pdb=" C ASP B 659 " ideal model delta sigma weight residual 111.28 120.99 -9.71 1.09e+00 8.42e-01 7.94e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 128.55 -8.99 1.02e+00 9.61e-01 7.76e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 128.53 -8.97 1.02e+00 9.61e-01 7.74e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.93 -8.37 1.01e+00 9.80e-01 6.88e+01 angle pdb=" C GLU D 492 " pdb=" N PRO D 493 " pdb=" CA PRO D 493 " ideal model delta sigma weight residual 119.56 127.96 -8.40 1.02e+00 9.61e-01 6.78e+01 ... (remaining 29997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 11980 17.56 - 35.12: 324 35.12 - 52.68: 100 52.68 - 70.24: 41 70.24 - 87.80: 20 Dihedral angle restraints: 12465 sinusoidal: 5002 harmonic: 7463 Sorted by residual: 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 93.00 159.59 -66.59 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.48 -66.48 1 1.00e+01 1.00e-02 5.77e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.78 -61.78 1 1.00e+01 1.00e-02 5.06e+01 ... (remaining 12462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2470 0.111 - 0.222: 758 0.222 - 0.333: 236 0.333 - 0.444: 127 0.444 - 0.555: 24 Chirality restraints: 3615 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.20e+02 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.06e+02 ... (remaining 3612 not shown) Planarity restraints: 3772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 706 " -0.226 2.00e-02 2.50e+03 1.89e-01 4.45e+02 pdb=" C7 NAG D 706 " 0.062 2.00e-02 2.50e+03 pdb=" C8 NAG D 706 " -0.159 2.00e-02 2.50e+03 pdb=" N2 NAG D 706 " 0.312 2.00e-02 2.50e+03 pdb=" O7 NAG D 706 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.172 2.00e-02 2.50e+03 1.42e-01 2.53e+02 pdb=" C7 NAG S 2 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.126 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.230 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 706 " 0.164 2.00e-02 2.50e+03 1.39e-01 2.40e+02 pdb=" C7 NAG C 706 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG C 706 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG C 706 " -0.224 2.00e-02 2.50e+03 pdb=" O7 NAG C 706 " 0.130 2.00e-02 2.50e+03 ... (remaining 3769 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5522 2.81 - 3.34: 19305 3.34 - 3.86: 35748 3.86 - 4.38: 42425 4.38 - 4.90: 69566 Nonbonded interactions: 172566 Sorted by model distance: nonbonded pdb=" O3 NAG E 702 " pdb=" O7 NAG E 702 " model vdw 2.293 3.040 nonbonded pdb=" N GLY L 50 " pdb=" O GLY L 50 " model vdw 2.370 2.496 nonbonded pdb=" O3 NAG S 2 " pdb=" O7 NAG S 2 " model vdw 2.385 3.040 nonbonded pdb=" NZ LYS A 207 " pdb=" OD2 ASP H 100C" model vdw 2.411 3.120 nonbonded pdb=" N ILE D 213 " pdb=" O ILE D 213 " model vdw 2.420 2.496 ... (remaining 172561 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' and (resid 33 through 504 or resid 701 through 713)) selection = (chain 'C' and (resid 33 through 57 or resid 66 through 185 or resid 189 through \ 504 or resid 702 through 714)) selection = (chain 'D' and (resid 33 through 57 or resid 66 through 185 or resid 189 through \ 504 or resid 701 through 713)) } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 3 through 106) selection = chain 'J' selection = (chain 'K' and resid 3 through 106) } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'U' selection = chain 'Y' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 3.490 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.850 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.024 0.163 22211 Z= 1.256 Angle : 1.765 13.201 30354 Z= 1.143 Chirality : 0.138 0.555 3615 Planarity : 0.010 0.189 3706 Dihedral : 10.440 87.795 7536 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 0.77 (0.16), residues: 2544 helix: -0.29 (0.22), residues: 447 sheet: 0.92 (0.17), residues: 749 loop : 0.73 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 192 TYR 0.057 0.007 TYR I 99 PHE 0.032 0.006 PHE G 71 TRP 0.064 0.009 TRP J 94 HIS 0.012 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02357 / 1.24 (22080) covalent geometry : angle 1.74087 / 1.14 (30002) SS BOND : bond 0.01044 / 0.62 ( 41) SS BOND : angle 2.64611 / 1.99 ( 82) hydrogen bonds : bond 0.16129 / 10.85 ( 839) hydrogen bonds : angle 7.83157 / 5.40 ( 2370) link_ALPHA1-3 : bond 0.08780 / 4.41 ( 3) link_ALPHA1-3 : angle 4.95621 / 2.91 ( 9) link_ALPHA1-6 : bond 0.05523 / 2.76 ( 3) link_ALPHA1-6 : angle 2.53294 / 1.51 ( 9) link_BETA1-4 : bond 0.07131 / 4.67 ( 18) link_BETA1-4 : angle 4.74893 / 3.29 ( 54) link_NAG-ASN : bond 0.07825 / 5.33 ( 66) link_NAG-ASN : angle 2.80073 / 1.96 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 585 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 82 ASP cc_start: 0.6977 (m-30) cc_final: 0.6200 (p0) REVERT: I 18 LEU cc_start: 0.8262 (mt) cc_final: 0.8020 (tp) REVERT: A 74 CYS cc_start: 0.8044 (p) cc_final: 0.7518 (t) REVERT: A 125 LEU cc_start: 0.9178 (mt) cc_final: 0.8972 (mt) REVERT: A 161 MET cc_start: 0.8663 (tpt) cc_final: 0.8096 (tpt) REVERT: A 198 THR cc_start: 0.9220 (m) cc_final: 0.9014 (p) REVERT: A 430 ILE cc_start: 0.9041 (mm) cc_final: 0.8776 (tp) REVERT: H 102 SER cc_start: 0.9118 (m) cc_final: 0.8840 (m) REVERT: M 32 ASN cc_start: 0.8006 (m-40) cc_final: 0.7350 (m-40) REVERT: M 101 ASP cc_start: 0.7811 (m-30) cc_final: 0.7585 (p0) REVERT: C 161 MET cc_start: 0.8726 (tpt) cc_final: 0.8505 (tpt) REVERT: K 69 THR cc_start: 0.6183 (p) cc_final: 0.5848 (t) REVERT: K 85 VAL cc_start: 0.8298 (t) cc_final: 0.8058 (p) REVERT: K 92 ASN cc_start: 0.8609 (p0) cc_final: 0.7385 (t0) REVERT: N 101 ASP cc_start: 0.8474 (m-30) cc_final: 0.7947 (m-30) REVERT: D 109 ILE cc_start: 0.9489 (mm) cc_final: 0.9270 (mt) REVERT: D 257 THR cc_start: 0.9299 (p) cc_final: 0.8961 (t) REVERT: F 659 ASP cc_start: 0.8672 (t70) cc_final: 0.8426 (t0) outliers start: 0 outliers final: 0 residues processed: 585 average time/residue: 0.1861 time to fit residues: 159.5397 Evaluate side-chains 308 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 HIS B 577 GLN H 105 GLN L 3 GLN L 32 GLN J 42 GLN C 280 ASN C 300 ASN C 352 HIS K 38 GLN ** K 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 33 ASN D 66 HIS D 300 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.099521 restraints weight = 37227.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102279 restraints weight = 20976.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104020 restraints weight = 14542.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105121 restraints weight = 11466.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105742 restraints weight = 9850.093| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22211 Z= 0.166 Angle : 0.745 10.659 30354 Z= 0.376 Chirality : 0.049 0.303 3615 Planarity : 0.005 0.041 3706 Dihedral : 5.066 20.988 2780 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.44 % Allowed : 7.91 % Favored : 90.65 % 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: 1.07 (0.16), residues: 2544 helix: 1.56 (0.27), residues: 410 sheet: 0.93 (0.18), residues: 755 loop : 0.44 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 444 TYR 0.017 0.002 TYR M 50 PHE 0.021 0.002 PHE G 98 TRP 0.017 0.002 TRP M 96 HIS 0.004 0.001 HIS E 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (22080) covalent geometry : angle 0.70179 / 0.37 (30002) SS BOND : bond 0.00456 / 0.27 ( 41) SS BOND : angle 1.09485 / 0.68 ( 82) hydrogen bonds : bond 0.05532 / 3.74 ( 839) hydrogen bonds : angle 5.90837 / 4.11 ( 2370) link_ALPHA1-3 : bond 0.01139 / 0.57 ( 3) link_ALPHA1-3 : angle 1.56647 / 1.11 ( 9) link_ALPHA1-6 : bond 0.00720 / 0.36 ( 3) link_ALPHA1-6 : angle 1.44248 / 0.97 ( 9) link_BETA1-4 : bond 0.00722 / 0.50 ( 18) link_BETA1-4 : angle 2.47605 / 1.71 ( 54) link_NAG-ASN : bond 0.00506 / 0.37 ( 66) link_NAG-ASN : angle 2.83551 / 1.96 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 401 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 18 LEU cc_start: 0.8180 (mt) cc_final: 0.7911 (tp) REVERT: A 46 LYS cc_start: 0.8911 (pttt) cc_final: 0.8645 (pttt) REVERT: A 74 CYS cc_start: 0.7166 (p) cc_final: 0.6838 (t) REVERT: A 430 ILE cc_start: 0.8934 (mm) cc_final: 0.8585 (tp) REVERT: B 535 MET cc_start: 0.7910 (mmp) cc_final: 0.7546 (mmt) REVERT: J 105 GLU cc_start: 0.6184 (tp30) cc_final: 0.5896 (tp30) REVERT: M 27 ASP cc_start: 0.5540 (t70) cc_final: 0.4717 (t70) REVERT: M 32 ASN cc_start: 0.7619 (m-40) cc_final: 0.6778 (m-40) REVERT: E 542 ARG cc_start: 0.7855 (mtm-85) cc_final: 0.7540 (mmm160) REVERT: E 661 LEU cc_start: 0.7913 (tp) cc_final: 0.7402 (mt) REVERT: K 85 VAL cc_start: 0.8097 (t) cc_final: 0.7780 (p) REVERT: K 92 ASN cc_start: 0.8068 (p0) cc_final: 0.7560 (t0) REVERT: N 33 ASN cc_start: 0.8136 (t0) cc_final: 0.7833 (t0) REVERT: N 43 LYS cc_start: 0.7384 (mtmt) cc_final: 0.6045 (mtpp) REVERT: N 81 LYS cc_start: 0.6783 (mptt) cc_final: 0.6517 (tttp) REVERT: N 101 ASP cc_start: 0.8166 (m-30) cc_final: 0.7699 (m-30) REVERT: D 46 LYS cc_start: 0.8634 (pttt) cc_final: 0.8361 (pttm) REVERT: D 257 THR cc_start: 0.9147 (p) cc_final: 0.8872 (t) outliers start: 33 outliers final: 19 residues processed: 420 average time/residue: 0.1685 time to fit residues: 107.3782 Evaluate side-chains 327 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 308 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 244 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 79 GLN C 185 ASN E 658 GLN K 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.117451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.095337 restraints weight = 37288.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.098001 restraints weight = 21548.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.099674 restraints weight = 15138.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.100750 restraints weight = 12048.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101362 restraints weight = 10380.922| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22211 Z= 0.217 Angle : 0.703 11.062 30354 Z= 0.352 Chirality : 0.049 0.363 3615 Planarity : 0.005 0.045 3706 Dihedral : 4.973 20.205 2780 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.40 % Allowed : 8.52 % Favored : 89.07 % 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: 0.71 (0.16), residues: 2544 helix: 1.38 (0.27), residues: 420 sheet: 0.79 (0.17), residues: 794 loop : 0.07 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 13 TYR 0.025 0.002 TYR J 49 PHE 0.018 0.002 PHE B 522 TRP 0.015 0.002 TRP M 96 HIS 0.005 0.002 HIS E 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (22080) covalent geometry : angle 0.67044 / 0.35 (30002) SS BOND : bond 0.00403 / 0.29 ( 41) SS BOND : angle 1.07633 / 0.64 ( 82) hydrogen bonds : bond 0.05019 / 3.36 ( 839) hydrogen bonds : angle 5.50128 / 3.84 ( 2370) link_ALPHA1-3 : bond 0.00576 / 0.29 ( 3) link_ALPHA1-3 : angle 1.57051 / 1.17 ( 9) link_ALPHA1-6 : bond 0.00500 / 0.25 ( 3) link_ALPHA1-6 : angle 1.47010 / 0.97 ( 9) link_BETA1-4 : bond 0.00575 / 0.38 ( 18) link_BETA1-4 : angle 1.88656 / 1.33 ( 54) link_NAG-ASN : bond 0.00380 / 0.26 ( 66) link_NAG-ASN : angle 2.44301 / 1.69 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 333 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7245 (p) cc_final: 0.6918 (t) REVERT: A 110 SER cc_start: 0.9196 (t) cc_final: 0.8726 (m) REVERT: A 161 MET cc_start: 0.8210 (tpp) cc_final: 0.7967 (tpt) REVERT: A 430 ILE cc_start: 0.9009 (mm) cc_final: 0.8647 (tp) REVERT: B 625 ASN cc_start: 0.8100 (m-40) cc_final: 0.7850 (p0) REVERT: M 27 ASP cc_start: 0.5895 (t70) cc_final: 0.4685 (t70) REVERT: M 32 ASN cc_start: 0.7844 (m-40) cc_final: 0.6928 (m110) REVERT: M 48 ILE cc_start: 0.7158 (mp) cc_final: 0.6861 (tp) REVERT: M 89 LYS cc_start: 0.7774 (tptp) cc_final: 0.7360 (tptp) REVERT: K 85 VAL cc_start: 0.8155 (t) cc_final: 0.7847 (p) REVERT: K 92 ASN cc_start: 0.8372 (p0) cc_final: 0.7429 (t0) REVERT: N 5 VAL cc_start: 0.7140 (p) cc_final: 0.6856 (t) REVERT: N 32 ASN cc_start: 0.8974 (m-40) cc_final: 0.8467 (m110) REVERT: N 43 LYS cc_start: 0.7645 (mtmt) cc_final: 0.6360 (mtpp) REVERT: N 101 ASP cc_start: 0.8188 (m-30) cc_final: 0.7696 (m-30) outliers start: 55 outliers final: 39 residues processed: 361 average time/residue: 0.1651 time to fit residues: 90.5971 Evaluate side-chains 325 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 286 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 221 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS C 185 ASN K 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.093794 restraints weight = 37320.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.096002 restraints weight = 22840.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098238 restraints weight = 16059.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.098456 restraints weight = 11723.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098585 restraints weight = 11539.663| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 22211 Z= 0.242 Angle : 0.700 11.281 30354 Z= 0.348 Chirality : 0.049 0.350 3615 Planarity : 0.005 0.046 3706 Dihedral : 5.003 21.185 2780 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.36 % Allowed : 10.45 % Favored : 87.19 % 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: 0.37 (0.16), residues: 2544 helix: 1.25 (0.27), residues: 420 sheet: 0.57 (0.18), residues: 802 loop : -0.22 (0.16), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 100B TYR 0.020 0.002 TYR J 49 PHE 0.014 0.002 PHE C 53 TRP 0.017 0.002 TRP M 96 HIS 0.006 0.002 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.24 (22080) covalent geometry : angle 0.66713 / 0.34 (30002) SS BOND : bond 0.00513 / 0.34 ( 41) SS BOND : angle 1.17359 / 0.81 ( 82) hydrogen bonds : bond 0.04910 / 3.27 ( 839) hydrogen bonds : angle 5.45037 / 3.79 ( 2370) link_ALPHA1-3 : bond 0.00455 / 0.22 ( 3) link_ALPHA1-3 : angle 1.72924 / 1.22 ( 9) link_ALPHA1-6 : bond 0.00343 / 0.17 ( 3) link_ALPHA1-6 : angle 1.51141 / 0.99 ( 9) link_BETA1-4 : bond 0.00507 / 0.34 ( 18) link_BETA1-4 : angle 1.79513 / 1.20 ( 54) link_NAG-ASN : bond 0.00340 / 0.23 ( 66) link_NAG-ASN : angle 2.43830 / 1.67 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 304 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7432 (p) cc_final: 0.7201 (t) REVERT: A 110 SER cc_start: 0.9209 (t) cc_final: 0.8708 (m) REVERT: A 161 MET cc_start: 0.8380 (tpp) cc_final: 0.8174 (tpt) REVERT: A 430 ILE cc_start: 0.9042 (mm) cc_final: 0.8696 (tp) REVERT: B 621 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7650 (mt-10) REVERT: B 625 ASN cc_start: 0.8275 (m-40) cc_final: 0.7893 (p0) REVERT: H 53 ASN cc_start: 0.9374 (t0) cc_final: 0.9173 (t0) REVERT: J 96 TRP cc_start: 0.8387 (m-10) cc_final: 0.8158 (m-10) REVERT: M 13 ARG cc_start: 0.5873 (mmm160) cc_final: 0.5054 (mmp-170) REVERT: M 27 ASP cc_start: 0.6085 (t70) cc_final: 0.4856 (t0) REVERT: M 32 ASN cc_start: 0.8001 (m-40) cc_final: 0.7167 (m110) REVERT: M 89 LYS cc_start: 0.7882 (tptp) cc_final: 0.7400 (tptp) REVERT: M 108 ARG cc_start: 0.4309 (ptt180) cc_final: 0.3980 (ptt180) REVERT: C 128 THR cc_start: 0.9126 (m) cc_final: 0.8923 (p) REVERT: E 634 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7509 (tm-30) REVERT: E 655 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8381 (mttp) REVERT: K 92 ASN cc_start: 0.8334 (p0) cc_final: 0.7368 (t0) REVERT: N 5 VAL cc_start: 0.7242 (p) cc_final: 0.6966 (t) REVERT: N 32 ASN cc_start: 0.8957 (m-40) cc_final: 0.8737 (m-40) REVERT: N 43 LYS cc_start: 0.7689 (mtmt) cc_final: 0.6283 (mtpp) REVERT: F 621 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7214 (tm-30) outliers start: 54 outliers final: 44 residues processed: 340 average time/residue: 0.1691 time to fit residues: 86.3062 Evaluate side-chains 330 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 285 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain E residue 655 LYS Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 136 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 241 optimal weight: 0.0570 chunk 243 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.096103 restraints weight = 37083.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.098745 restraints weight = 21345.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100410 restraints weight = 14974.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.101474 restraints weight = 11907.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102033 restraints weight = 10251.987| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22211 Z= 0.132 Angle : 0.606 9.705 30354 Z= 0.302 Chirality : 0.046 0.306 3615 Planarity : 0.004 0.050 3706 Dihedral : 4.698 19.739 2780 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.75 % Allowed : 11.54 % Favored : 86.71 % 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: 0.47 (0.16), residues: 2544 helix: 1.58 (0.27), residues: 420 sheet: 0.61 (0.18), residues: 793 loop : -0.22 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 13 TYR 0.014 0.001 TYR N 50 PHE 0.012 0.001 PHE D 53 TRP 0.018 0.001 TRP M 36 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (22080) covalent geometry : angle 0.57549 / 0.30 (30002) SS BOND : bond 0.00394 / 0.23 ( 41) SS BOND : angle 1.10882 / 0.73 ( 82) hydrogen bonds : bond 0.04117 / 2.76 ( 839) hydrogen bonds : angle 5.10622 / 3.56 ( 2370) link_ALPHA1-3 : bond 0.00569 / 0.28 ( 3) link_ALPHA1-3 : angle 1.52841 / 1.13 ( 9) link_ALPHA1-6 : bond 0.00399 / 0.20 ( 3) link_ALPHA1-6 : angle 1.40135 / 0.98 ( 9) link_BETA1-4 : bond 0.00511 / 0.35 ( 18) link_BETA1-4 : angle 1.45434 / 0.95 ( 54) link_NAG-ASN : bond 0.00299 / 0.21 ( 66) link_NAG-ASN : angle 2.21555 / 1.52 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 328 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7295 (p) cc_final: 0.6992 (t) REVERT: A 110 SER cc_start: 0.9060 (t) cc_final: 0.8606 (m) REVERT: A 430 ILE cc_start: 0.9002 (mm) cc_final: 0.8688 (tp) REVERT: B 625 ASN cc_start: 0.8152 (m-40) cc_final: 0.7879 (p0) REVERT: M 13 ARG cc_start: 0.6445 (mmm160) cc_final: 0.6114 (mmm160) REVERT: M 27 ASP cc_start: 0.5906 (t70) cc_final: 0.4624 (t0) REVERT: M 32 ASN cc_start: 0.7914 (m-40) cc_final: 0.7314 (m110) REVERT: M 89 LYS cc_start: 0.7806 (tptp) cc_final: 0.7433 (tptp) REVERT: E 634 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7445 (tm-30) REVERT: K 92 ASN cc_start: 0.8064 (p0) cc_final: 0.7266 (t0) REVERT: N 5 VAL cc_start: 0.7196 (p) cc_final: 0.6995 (t) REVERT: N 32 ASN cc_start: 0.8975 (m-40) cc_final: 0.8519 (m110) REVERT: N 43 LYS cc_start: 0.7548 (mtmt) cc_final: 0.6192 (mtpp) REVERT: D 46 LYS cc_start: 0.8607 (pttt) cc_final: 0.8390 (pttm) REVERT: F 621 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7127 (tm-30) outliers start: 40 outliers final: 30 residues processed: 352 average time/residue: 0.1785 time to fit residues: 93.4745 Evaluate side-chains 326 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 296 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 233 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 243 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 231 optimal weight: 8.9990 chunk 200 optimal weight: 0.0980 chunk 197 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN C 103 GLN C 185 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.093212 restraints weight = 37464.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.095816 restraints weight = 21695.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.097464 restraints weight = 15287.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.098516 restraints weight = 12191.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.099161 restraints weight = 10511.401| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22211 Z= 0.217 Angle : 0.665 7.583 30354 Z= 0.328 Chirality : 0.048 0.338 3615 Planarity : 0.004 0.052 3706 Dihedral : 4.817 20.204 2780 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.53 % Allowed : 12.06 % Favored : 85.40 % 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: 0.25 (0.16), residues: 2544 helix: 1.41 (0.27), residues: 420 sheet: 0.49 (0.18), residues: 802 loop : -0.40 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 480 TYR 0.019 0.002 TYR J 49 PHE 0.014 0.002 PHE I 78 TRP 0.014 0.001 TRP M 96 HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (22080) covalent geometry : angle 0.63304 / 0.32 (30002) SS BOND : bond 0.00416 / 0.30 ( 41) SS BOND : angle 1.17003 / 0.78 ( 82) hydrogen bonds : bond 0.04616 / 3.08 ( 839) hydrogen bonds : angle 5.23607 / 3.65 ( 2370) link_ALPHA1-3 : bond 0.00463 / 0.23 ( 3) link_ALPHA1-3 : angle 1.77236 / 1.24 ( 9) link_ALPHA1-6 : bond 0.00316 / 0.16 ( 3) link_ALPHA1-6 : angle 1.53761 / 1.03 ( 9) link_BETA1-4 : bond 0.00467 / 0.31 ( 18) link_BETA1-4 : angle 1.68596 / 1.12 ( 54) link_NAG-ASN : bond 0.00331 / 0.23 ( 66) link_NAG-ASN : angle 2.33435 / 1.61 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 297 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 58 ARG cc_start: 0.7321 (mtm180) cc_final: 0.6939 (mtm180) REVERT: A 110 SER cc_start: 0.9166 (t) cc_final: 0.8751 (m) REVERT: A 430 ILE cc_start: 0.9023 (mm) cc_final: 0.8750 (tp) REVERT: B 621 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7633 (mt-10) REVERT: B 625 ASN cc_start: 0.8147 (m-40) cc_final: 0.7883 (p0) REVERT: M 13 ARG cc_start: 0.6356 (mmm160) cc_final: 0.5764 (mmm160) REVERT: M 27 ASP cc_start: 0.6043 (t70) cc_final: 0.4798 (t0) REVERT: M 32 ASN cc_start: 0.7885 (m-40) cc_final: 0.7300 (m110) REVERT: M 89 LYS cc_start: 0.7875 (tptp) cc_final: 0.7598 (tptp) REVERT: E 634 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7508 (tm-30) REVERT: K 87 PHE cc_start: 0.8350 (m-80) cc_final: 0.8088 (m-80) REVERT: N 5 VAL cc_start: 0.7331 (p) cc_final: 0.7114 (t) REVERT: N 32 ASN cc_start: 0.9017 (m-40) cc_final: 0.8731 (m-40) REVERT: N 33 ASN cc_start: 0.8462 (t0) cc_final: 0.8129 (t0) REVERT: N 43 LYS cc_start: 0.7492 (mtmt) cc_final: 0.6163 (mtpp) REVERT: N 77 GLN cc_start: 0.7314 (pp30) cc_final: 0.6968 (pp30) outliers start: 58 outliers final: 39 residues processed: 332 average time/residue: 0.1785 time to fit residues: 88.8354 Evaluate side-chains 326 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 287 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 199 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 218 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 37 optimal weight: 0.0470 chunk 17 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 32 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** 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 = 0.3481 r_free = 0.3481 target = 0.117021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.095351 restraints weight = 37201.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.097964 restraints weight = 21455.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099631 restraints weight = 15047.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.100712 restraints weight = 11990.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101279 restraints weight = 10306.541| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22211 Z= 0.142 Angle : 0.601 7.810 30354 Z= 0.299 Chirality : 0.046 0.301 3615 Planarity : 0.004 0.058 3706 Dihedral : 4.617 19.266 2780 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.53 % Allowed : 13.24 % Favored : 85.23 % 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: 0.28 (0.16), residues: 2544 helix: 1.60 (0.27), residues: 420 sheet: 0.47 (0.18), residues: 805 loop : -0.41 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 100B TYR 0.013 0.001 TYR N 50 PHE 0.012 0.002 PHE I 100C TRP 0.014 0.001 TRP J 94 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (22080) covalent geometry : angle 0.57241 / 0.29 (30002) SS BOND : bond 0.00303 / 0.20 ( 41) SS BOND : angle 0.94168 / 0.65 ( 82) hydrogen bonds : bond 0.04033 / 2.69 ( 839) hydrogen bonds : angle 5.01572 / 3.50 ( 2370) link_ALPHA1-3 : bond 0.00541 / 0.26 ( 3) link_ALPHA1-3 : angle 1.57375 / 1.17 ( 9) link_ALPHA1-6 : bond 0.00339 / 0.17 ( 3) link_ALPHA1-6 : angle 1.43742 / 1.01 ( 9) link_BETA1-4 : bond 0.00469 / 0.32 ( 18) link_BETA1-4 : angle 1.42678 / 0.92 ( 54) link_NAG-ASN : bond 0.00295 / 0.21 ( 66) link_NAG-ASN : angle 2.15568 / 1.47 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 303 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.9097 (t) cc_final: 0.8708 (m) REVERT: A 430 ILE cc_start: 0.8987 (mm) cc_final: 0.8735 (tp) REVERT: B 621 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7523 (mt-10) REVERT: M 27 ASP cc_start: 0.6053 (t70) cc_final: 0.4774 (t0) REVERT: M 32 ASN cc_start: 0.7897 (m-40) cc_final: 0.7355 (m110) REVERT: M 89 LYS cc_start: 0.7851 (tptp) cc_final: 0.7608 (tptp) REVERT: E 634 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7519 (tm-30) REVERT: K 87 PHE cc_start: 0.8301 (m-80) cc_final: 0.8090 (m-80) REVERT: N 5 VAL cc_start: 0.7337 (p) cc_final: 0.7123 (t) REVERT: N 32 ASN cc_start: 0.9033 (m-40) cc_final: 0.8762 (m-40) REVERT: N 33 ASN cc_start: 0.8441 (t0) cc_final: 0.8111 (t0) REVERT: N 43 LYS cc_start: 0.7358 (mtmt) cc_final: 0.6018 (mtpp) REVERT: N 71 THR cc_start: 0.7512 (OUTLIER) cc_final: 0.7304 (m) REVERT: N 77 GLN cc_start: 0.7392 (pp30) cc_final: 0.6975 (pp30) outliers start: 35 outliers final: 30 residues processed: 326 average time/residue: 0.1832 time to fit residues: 88.8475 Evaluate side-chains 318 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 287 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 225 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN C 103 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** 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 = 0.3461 r_free = 0.3461 target = 0.115676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.094072 restraints weight = 37339.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.096645 restraints weight = 21577.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.098295 restraints weight = 15187.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099340 restraints weight = 12069.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099901 restraints weight = 10411.815| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22211 Z= 0.191 Angle : 0.639 8.537 30354 Z= 0.316 Chirality : 0.047 0.320 3615 Planarity : 0.004 0.059 3706 Dihedral : 4.693 19.774 2780 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.75 % Allowed : 13.11 % Favored : 85.14 % 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: 0.19 (0.16), residues: 2544 helix: 1.52 (0.27), residues: 420 sheet: 0.44 (0.18), residues: 804 loop : -0.50 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 166 TYR 0.017 0.001 TYR J 49 PHE 0.013 0.002 PHE M 78 TRP 0.017 0.001 TRP J 94 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (22080) covalent geometry : angle 0.61077 / 0.31 (30002) SS BOND : bond 0.00331 / 0.23 ( 41) SS BOND : angle 0.88657 / 0.59 ( 82) hydrogen bonds : bond 0.04306 / 2.87 ( 839) hydrogen bonds : angle 5.07449 / 3.54 ( 2370) link_ALPHA1-3 : bond 0.00429 / 0.21 ( 3) link_ALPHA1-3 : angle 1.68500 / 1.22 ( 9) link_ALPHA1-6 : bond 0.00327 / 0.16 ( 3) link_ALPHA1-6 : angle 1.50755 / 1.02 ( 9) link_BETA1-4 : bond 0.00462 / 0.31 ( 18) link_BETA1-4 : angle 1.54761 / 1.02 ( 54) link_NAG-ASN : bond 0.00310 / 0.21 ( 66) link_NAG-ASN : angle 2.19553 / 1.49 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 289 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 SER cc_start: 0.9131 (t) cc_final: 0.8740 (m) REVERT: A 430 ILE cc_start: 0.8981 (mm) cc_final: 0.8748 (tp) REVERT: M 27 ASP cc_start: 0.6068 (t70) cc_final: 0.4738 (t0) REVERT: M 32 ASN cc_start: 0.7860 (m-40) cc_final: 0.7392 (m110) REVERT: M 89 LYS cc_start: 0.7875 (tptp) cc_final: 0.7604 (tptp) REVERT: M 108 ARG cc_start: 0.4188 (ptt180) cc_final: 0.3803 (ptt180) REVERT: E 634 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7533 (tm-30) REVERT: K 87 PHE cc_start: 0.8285 (m-80) cc_final: 0.8060 (m-80) REVERT: K 93 ASP cc_start: 0.7814 (p0) cc_final: 0.7414 (p0) REVERT: N 3 GLN cc_start: 0.7731 (pm20) cc_final: 0.7431 (pm20) REVERT: N 5 VAL cc_start: 0.7404 (p) cc_final: 0.7192 (t) REVERT: N 32 ASN cc_start: 0.9029 (m-40) cc_final: 0.8696 (m110) REVERT: N 43 LYS cc_start: 0.7282 (mtmt) cc_final: 0.6048 (mtpp) REVERT: N 46 GLU cc_start: 0.6569 (tp30) cc_final: 0.6214 (tm-30) REVERT: N 71 THR cc_start: 0.7451 (OUTLIER) cc_final: 0.7240 (m) REVERT: N 77 GLN cc_start: 0.7350 (pp30) cc_final: 0.6908 (pp30) outliers start: 40 outliers final: 36 residues processed: 313 average time/residue: 0.1741 time to fit residues: 81.9675 Evaluate side-chains 319 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 282 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 222 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN L 3 GLN L 30 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** 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 = 0.3495 r_free = 0.3495 target = 0.118033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096464 restraints weight = 37264.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099099 restraints weight = 21368.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100780 restraints weight = 14942.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.101783 restraints weight = 11842.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.102486 restraints weight = 10242.885| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22211 Z= 0.114 Angle : 0.583 8.651 30354 Z= 0.291 Chirality : 0.045 0.282 3615 Planarity : 0.004 0.061 3706 Dihedral : 4.460 18.392 2780 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.57 % Allowed : 13.37 % Favored : 85.05 % 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: 0.35 (0.17), residues: 2544 helix: 1.77 (0.27), residues: 417 sheet: 0.51 (0.18), residues: 824 loop : -0.42 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 66 TYR 0.013 0.001 TYR N 50 PHE 0.012 0.001 PHE M 78 TRP 0.022 0.001 TRP J 94 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (22080) covalent geometry : angle 0.55764 / 0.29 (30002) SS BOND : bond 0.00367 / 0.20 ( 41) SS BOND : angle 0.85516 / 0.55 ( 82) hydrogen bonds : bond 0.03673 / 2.44 ( 839) hydrogen bonds : angle 4.84019 / 3.38 ( 2370) link_ALPHA1-3 : bond 0.00509 / 0.25 ( 3) link_ALPHA1-3 : angle 1.51074 / 1.15 ( 9) link_ALPHA1-6 : bond 0.00344 / 0.17 ( 3) link_ALPHA1-6 : angle 1.40081 / 1.02 ( 9) link_BETA1-4 : bond 0.00456 / 0.31 ( 18) link_BETA1-4 : angle 1.29483 / 0.83 ( 54) link_NAG-ASN : bond 0.00296 / 0.21 ( 66) link_NAG-ASN : angle 1.99459 / 1.34 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 307 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 103 LYS cc_start: 0.6764 (ttmm) cc_final: 0.6505 (tppt) REVERT: I 70 SER cc_start: 0.8391 (t) cc_final: 0.8059 (m) REVERT: A 110 SER cc_start: 0.8993 (t) cc_final: 0.8613 (m) REVERT: A 430 ILE cc_start: 0.9025 (mm) cc_final: 0.8787 (tp) REVERT: M 27 ASP cc_start: 0.5951 (t70) cc_final: 0.4742 (t70) REVERT: M 32 ASN cc_start: 0.7874 (m-40) cc_final: 0.7278 (m110) REVERT: M 100 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8549 (ttmt) REVERT: M 108 ARG cc_start: 0.4305 (ptt180) cc_final: 0.3924 (ptt180) REVERT: E 634 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7526 (tm-30) REVERT: N 3 GLN cc_start: 0.7789 (pm20) cc_final: 0.7497 (pm20) REVERT: N 32 ASN cc_start: 0.8994 (m-40) cc_final: 0.8689 (m110) REVERT: N 43 LYS cc_start: 0.6944 (mtmt) cc_final: 0.6072 (mtpp) REVERT: N 46 GLU cc_start: 0.6504 (tp30) cc_final: 0.6271 (tm-30) outliers start: 36 outliers final: 30 residues processed: 329 average time/residue: 0.1728 time to fit residues: 85.8020 Evaluate side-chains 328 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 298 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 228 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 241 optimal weight: 0.0000 chunk 94 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 overall best weight: 2.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN L 3 GLN L 30 ASN C 185 ASN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.115135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.093472 restraints weight = 37438.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.096039 restraints weight = 21688.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.097663 restraints weight = 15279.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098699 restraints weight = 12172.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.099188 restraints weight = 10509.216| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22211 Z= 0.216 Angle : 0.667 9.206 30354 Z= 0.330 Chirality : 0.048 0.317 3615 Planarity : 0.004 0.059 3706 Dihedral : 4.696 20.561 2780 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.57 % Allowed : 13.72 % Favored : 84.70 % 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: 0.20 (0.17), residues: 2544 helix: 1.52 (0.27), residues: 422 sheet: 0.48 (0.18), residues: 803 loop : -0.51 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 66 TYR 0.017 0.002 TYR J 49 PHE 0.014 0.002 PHE I 78 TRP 0.022 0.001 TRP J 94 HIS 0.005 0.001 HIS H 100F Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (22080) covalent geometry : angle 0.64096 / 0.33 (30002) SS BOND : bond 0.00408 / 0.27 ( 41) SS BOND : angle 0.94259 / 0.60 ( 82) hydrogen bonds : bond 0.04388 / 2.92 ( 839) hydrogen bonds : angle 5.10744 / 3.57 ( 2370) link_ALPHA1-3 : bond 0.00501 / 0.24 ( 3) link_ALPHA1-3 : angle 1.80609 / 1.27 ( 9) link_ALPHA1-6 : bond 0.00315 / 0.16 ( 3) link_ALPHA1-6 : angle 1.53341 / 1.03 ( 9) link_BETA1-4 : bond 0.00451 / 0.30 ( 18) link_BETA1-4 : angle 1.56978 / 1.04 ( 54) link_NAG-ASN : bond 0.00323 / 0.22 ( 66) link_NAG-ASN : angle 2.15635 / 1.46 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 281 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 103 LYS cc_start: 0.6789 (ttmm) cc_final: 0.6414 (ttmt) REVERT: A 110 SER cc_start: 0.9144 (t) cc_final: 0.8747 (m) REVERT: A 430 ILE cc_start: 0.9005 (mm) cc_final: 0.8781 (tp) REVERT: M 27 ASP cc_start: 0.6030 (t70) cc_final: 0.4835 (t0) REVERT: M 32 ASN cc_start: 0.7823 (m-40) cc_final: 0.7198 (m110) REVERT: M 108 ARG cc_start: 0.4486 (ptt180) cc_final: 0.4239 (ptt180) REVERT: E 634 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7576 (tm-30) REVERT: N 32 ASN cc_start: 0.8991 (m-40) cc_final: 0.8721 (m110) REVERT: N 43 LYS cc_start: 0.7169 (mtmt) cc_final: 0.6033 (mtpp) outliers start: 36 outliers final: 30 residues processed: 304 average time/residue: 0.1685 time to fit residues: 76.9536 Evaluate side-chains 305 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 275 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 198 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 250 optimal weight: 0.8980 chunk 247 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 30 ASN C 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.093050 restraints weight = 37731.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.095619 restraints weight = 21771.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.097263 restraints weight = 15319.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098280 restraints weight = 12201.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.098838 restraints weight = 10546.406| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22211 Z= 0.208 Angle : 0.658 9.221 30354 Z= 0.325 Chirality : 0.048 0.308 3615 Planarity : 0.004 0.067 3706 Dihedral : 4.757 20.771 2780 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.44 % Allowed : 14.07 % Favored : 84.48 % 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: 0.05 (0.16), residues: 2544 helix: 1.40 (0.27), residues: 422 sheet: 0.40 (0.18), residues: 803 loop : -0.62 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 66 TYR 0.016 0.002 TYR J 49 PHE 0.014 0.002 PHE I 78 TRP 0.023 0.001 TRP J 94 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (22080) covalent geometry : angle 0.63136 / 0.32 (30002) SS BOND : bond 0.00392 / 0.26 ( 41) SS BOND : angle 0.89927 / 0.57 ( 82) hydrogen bonds : bond 0.04364 / 2.90 ( 839) hydrogen bonds : angle 5.12863 / 3.59 ( 2370) link_ALPHA1-3 : bond 0.00458 / 0.22 ( 3) link_ALPHA1-3 : angle 1.74797 / 1.26 ( 9) link_ALPHA1-6 : bond 0.00299 / 0.15 ( 3) link_ALPHA1-6 : angle 1.54360 / 1.03 ( 9) link_BETA1-4 : bond 0.00450 / 0.30 ( 18) link_BETA1-4 : angle 1.54879 / 1.00 ( 54) link_NAG-ASN : bond 0.00308 / 0.21 ( 66) link_NAG-ASN : angle 2.19544 / 1.49 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3803.39 seconds wall clock time: 66 minutes 42.23 seconds (4002.23 seconds total)