Starting phenix.real_space_refine on Thu Aug 6 21:09:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n0d_48781/08_2026/9n0d_48781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n0d_48781/08_2026/9n0d_48781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n0d_48781/08_2026/9n0d_48781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n0d_48781/08_2026/9n0d_48781.map" model { file = "/net/cci-nas-00/data/ceres_data/9n0d_48781/08_2026/9n0d_48781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n0d_48781/08_2026/9n0d_48781.cif" } resolution = 3.8 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= -0.006 sd= 0.106 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 123 5.16 5 C 10869 2.51 5 N 2820 2.21 5 O 3177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16989 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 441 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "B" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1517 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 11, 'TRANS': 175} Chain: "C" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1829 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Chain: "D" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 796 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain breaks: 1 Chain: "F" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 441 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "G" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1517 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 11, 'TRANS': 175} Chain: "H" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1829 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Chain: "I" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 796 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain breaks: 1 Chain: "K" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 441 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "L" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1517 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 11, 'TRANS': 175} Chain: "M" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1829 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Chain: "N" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 796 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "O" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain breaks: 1 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.91, per 1000 atoms: 0.17 Number of scatterers: 16989 At special positions: 0 Unit cell: (133.63, 124.5, 180.94, 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 123 16.00 O 3177 8.00 N 2820 7.00 C 10869 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS C 469 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 271 " - pdb=" SG CYS C 284 " distance=2.04 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 302 " distance=2.03 Simple disulfide: pdb=" SG CYS C 356 " - pdb=" SG CYS C 377 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS H 469 " distance=2.03 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 226 " distance=2.03 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 164 " distance=2.03 Simple disulfide: pdb=" SG CYS G 207 " - pdb=" SG CYS G 213 " distance=2.03 Simple disulfide: pdb=" SG CYS H 271 " - pdb=" SG CYS H 284 " distance=2.04 Simple disulfide: pdb=" SG CYS H 293 " - pdb=" SG CYS H 302 " distance=2.03 Simple disulfide: pdb=" SG CYS H 356 " - pdb=" SG CYS H 377 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 87 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 57 " - pdb=" SG CYS M 469 " distance=2.03 Simple disulfide: pdb=" SG CYS L 92 " - pdb=" SG CYS L 226 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 164 " distance=2.03 Simple disulfide: pdb=" SG CYS L 207 " - pdb=" SG CYS L 213 " distance=2.03 Simple disulfide: pdb=" SG CYS M 271 " - pdb=" SG CYS M 284 " distance=2.04 Simple disulfide: pdb=" SG CYS M 293 " - pdb=" SG CYS M 302 " distance=2.03 Simple disulfide: pdb=" SG CYS M 356 " - pdb=" SG CYS M 377 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 87 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.04 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=3, symmetry=0 Links applied BETA1-4 " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " NAG-ASN " NAG B 301 " - " ASN B 95 " " NAG B 302 " - " ASN B 166 " " NAG C 501 " - " ASN C 365 " " NAG C 502 " - " ASN C 382 " " NAG C 503 " - " ASN C 387 " " NAG G 301 " - " ASN G 95 " " NAG G 302 " - " ASN G 166 " " NAG H 501 " - " ASN H 365 " " NAG H 502 " - " ASN H 382 " " NAG H 503 " - " ASN H 387 " " NAG L 301 " - " ASN L 95 " " NAG L 302 " - " ASN L 166 " " NAG M 501 " - " ASN M 365 " " NAG M 502 " - " ASN M 382 " " NAG M 503 " - " ASN M 387 " " NAG R 1 " - " ASN B 178 " " NAG W 1 " - " ASN G 178 " " NAG Y 1 " - " ASN C 357 " " NAG b 1 " - " ASN L 178 " " NAG h 1 " - " ASN H 357 " " NAG n 1 " - " ASN M 357 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 737.6 milliseconds 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3876 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 33 sheets defined 33.8% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 removed outlier: 3.905A pdb=" N SER A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) Proline residue: A 12 - end of helix Processing helix chain 'A' and resid 17 through 42 Processing helix chain 'A' and resid 42 through 53 Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.633A pdb=" N ILE B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 Processing helix chain 'B' and resid 230 through 240 Processing helix chain 'C' and resid 273 through 277 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 292 through 295 removed outlier: 4.424A pdb=" N LEU C 295 " --> pdb=" O LYS C 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 292 through 295' Processing helix chain 'C' and resid 299 through 321 Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 338 through 351 removed outlier: 3.546A pdb=" N MET C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 391 through 416 removed outlier: 4.285A pdb=" N TRP C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU C 397 " --> pdb=" O ASN C 393 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG C 414 " --> pdb=" O GLU C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 443 removed outlier: 3.519A pdb=" N VAL C 423 " --> pdb=" O PRO C 419 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY C 443 " --> pdb=" O LEU C 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 3 through 15 Proline residue: F 12 - end of helix Processing helix chain 'F' and resid 17 through 42 Processing helix chain 'F' and resid 42 through 53 Processing helix chain 'G' and resid 77 through 84 Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'G' and resid 138 through 153 removed outlier: 3.633A pdb=" N ILE G 142 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 200 Processing helix chain 'G' and resid 230 through 240 Processing helix chain 'H' and resid 273 through 277 Processing helix chain 'H' and resid 286 through 291 Processing helix chain 'H' and resid 292 through 295 removed outlier: 4.424A pdb=" N LEU H 295 " --> pdb=" O LYS H 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 292 through 295' Processing helix chain 'H' and resid 299 through 321 Processing helix chain 'H' and resid 329 through 337 Processing helix chain 'H' and resid 338 through 351 removed outlier: 3.545A pdb=" N MET H 351 " --> pdb=" O ILE H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 390 Processing helix chain 'H' and resid 391 through 416 removed outlier: 4.285A pdb=" N TRP H 395 " --> pdb=" O PHE H 391 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE H 396 " --> pdb=" O ARG H 392 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU H 397 " --> pdb=" O ASN H 393 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG H 414 " --> pdb=" O GLU H 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 419 through 443 removed outlier: 3.519A pdb=" N VAL H 423 " --> pdb=" O PRO H 419 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY H 443 " --> pdb=" O LEU H 439 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 3 through 15 Proline residue: K 12 - end of helix Processing helix chain 'K' and resid 17 through 42 Processing helix chain 'K' and resid 42 through 53 Processing helix chain 'L' and resid 77 through 84 Processing helix chain 'L' and resid 130 through 135 Processing helix chain 'L' and resid 138 through 153 removed outlier: 3.633A pdb=" N ILE L 142 " --> pdb=" O SER L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 200 Processing helix chain 'L' and resid 230 through 240 Processing helix chain 'M' and resid 273 through 277 Processing helix chain 'M' and resid 286 through 291 Processing helix chain 'M' and resid 292 through 295 removed outlier: 4.424A pdb=" N LEU M 295 " --> pdb=" O LYS M 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 292 through 295' Processing helix chain 'M' and resid 299 through 321 Processing helix chain 'M' and resid 329 through 337 Processing helix chain 'M' and resid 338 through 351 removed outlier: 3.546A pdb=" N MET M 351 " --> pdb=" O ILE M 347 " (cutoff:3.500A) Processing helix chain 'M' and resid 387 through 390 Processing helix chain 'M' and resid 391 through 416 removed outlier: 4.285A pdb=" N TRP M 395 " --> pdb=" O PHE M 391 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE M 396 " --> pdb=" O ARG M 392 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU M 397 " --> pdb=" O ASN M 393 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG M 414 " --> pdb=" O GLU M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 419 through 443 removed outlier: 3.519A pdb=" N VAL M 423 " --> pdb=" O PRO M 419 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY M 443 " --> pdb=" O LEU M 439 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 65 Processing helix chain 'O' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 62 through 64 removed outlier: 3.581A pdb=" N THR B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 94 removed outlier: 3.623A pdb=" N GLN B 176 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 163 " --> pdb=" O GLN B 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 271 through 272 Processing sheet with id=AA4, first strand: chain 'C' and resid 380 through 381 Processing sheet with id=AA5, first strand: chain 'C' and resid 447 through 450 Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 13 removed outlier: 5.830A pdb=" N MET D 11 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP D 34 " --> pdb=" O TRP D 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13 removed outlier: 5.830A pdb=" N MET D 11 " --> pdb=" O GLU D 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.222A pdb=" N GLY E 10 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET E 34 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG E 44 " --> pdb=" O THR E 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.222A pdb=" N GLY E 10 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N CYS E 96 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TRP E 112 " --> pdb=" O CYS E 96 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 17 through 22 Processing sheet with id=AB3, first strand: chain 'G' and resid 62 through 64 removed outlier: 3.582A pdb=" N THR G 68 " --> pdb=" O ILE G 64 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 90 through 94 removed outlier: 3.623A pdb=" N GLN G 176 " --> pdb=" O LEU G 163 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU G 163 " --> pdb=" O GLN G 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 271 through 272 Processing sheet with id=AB6, first strand: chain 'H' and resid 380 through 381 Processing sheet with id=AB7, first strand: chain 'H' and resid 447 through 450 Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 13 removed outlier: 5.830A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP I 34 " --> pdb=" O TRP I 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 10 through 13 removed outlier: 5.830A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.222A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET J 34 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG J 44 " --> pdb=" O THR J 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.222A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N CYS J 96 " --> pdb=" O TRP J 112 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TRP J 112 " --> pdb=" O CYS J 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 17 through 22 Processing sheet with id=AC5, first strand: chain 'L' and resid 62 through 64 removed outlier: 3.581A pdb=" N THR L 68 " --> pdb=" O ILE L 64 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 90 through 94 removed outlier: 3.623A pdb=" N GLN L 176 " --> pdb=" O LEU L 163 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU L 163 " --> pdb=" O GLN L 176 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 271 through 272 Processing sheet with id=AC8, first strand: chain 'M' and resid 380 through 381 Processing sheet with id=AC9, first strand: chain 'M' and resid 447 through 450 Processing sheet with id=AD1, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'N' and resid 10 through 13 removed outlier: 5.829A pdb=" N MET N 11 " --> pdb=" O GLU N 104 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP N 34 " --> pdb=" O TRP N 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 10 through 13 removed outlier: 5.829A pdb=" N MET N 11 " --> pdb=" O GLU N 104 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.223A pdb=" N GLY O 10 " --> pdb=" O THR O 119 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET O 34 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG O 44 " --> pdb=" O THR O 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.223A pdb=" N GLY O 10 " --> pdb=" O THR O 119 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N CYS O 96 " --> pdb=" O TRP O 112 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TRP O 112 " --> pdb=" O CYS O 96 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 17 through 22 792 hydrogen bonds defined for protein. 2061 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: 2.55 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5229 1.34 - 1.46: 4376 1.46 - 1.58: 7621 1.58 - 1.70: 0 1.70 - 1.82: 183 Bond restraints: 17409 Sorted by residual: bond pdb=" CB ASP J 42 " pdb=" CG ASP J 42 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.21e+00 bond pdb=" CB ASP E 42 " pdb=" CG ASP E 42 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.20e+00 bond pdb=" CB ASP O 42 " pdb=" CG ASP O 42 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.18e+00 bond pdb=" CA ASP J 42 " pdb=" CB ASP J 42 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.66e-02 3.63e+03 1.00e+00 bond pdb=" CA ASP E 42 " pdb=" CB ASP E 42 " ideal model delta sigma weight residual 1.528 1.545 -0.016 1.66e-02 3.63e+03 9.70e-01 ... (remaining 17404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.45: 23466 4.45 - 8.90: 87 8.90 - 13.35: 3 13.35 - 17.81: 6 17.81 - 22.26: 3 Bond angle restraints: 23565 Sorted by residual: angle pdb=" C ALA G 106 " pdb=" CA ALA G 106 " pdb=" CB ALA G 106 " ideal model delta sigma weight residual 109.70 87.44 22.26 1.81e+00 3.05e-01 1.51e+02 angle pdb=" C ALA L 106 " pdb=" CA ALA L 106 " pdb=" CB ALA L 106 " ideal model delta sigma weight residual 109.70 87.46 22.24 1.81e+00 3.05e-01 1.51e+02 angle pdb=" C ALA B 106 " pdb=" CA ALA B 106 " pdb=" CB ALA B 106 " ideal model delta sigma weight residual 109.70 87.46 22.24 1.81e+00 3.05e-01 1.51e+02 angle pdb=" N ALA L 106 " pdb=" CA ALA L 106 " pdb=" C ALA L 106 " ideal model delta sigma weight residual 108.76 91.00 17.76 1.69e+00 3.50e-01 1.10e+02 angle pdb=" N ALA B 106 " pdb=" CA ALA B 106 " pdb=" C ALA B 106 " ideal model delta sigma weight residual 108.76 91.00 17.76 1.69e+00 3.50e-01 1.10e+02 ... (remaining 23560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.88: 8556 13.88 - 27.76: 1261 27.76 - 41.63: 659 41.63 - 55.51: 231 55.51 - 69.39: 60 Dihedral angle restraints: 10767 sinusoidal: 4743 harmonic: 6024 Sorted by residual: dihedral pdb=" C ALA G 106 " pdb=" N ALA G 106 " pdb=" CA ALA G 106 " pdb=" CB ALA G 106 " ideal model delta harmonic sigma weight residual -122.60 -87.65 -34.95 0 2.50e+00 1.60e-01 1.95e+02 dihedral pdb=" C ALA L 106 " pdb=" N ALA L 106 " pdb=" CA ALA L 106 " pdb=" CB ALA L 106 " ideal model delta harmonic sigma weight residual -122.60 -87.66 -34.94 0 2.50e+00 1.60e-01 1.95e+02 dihedral pdb=" C ALA B 106 " pdb=" N ALA B 106 " pdb=" CA ALA B 106 " pdb=" CB ALA B 106 " ideal model delta harmonic sigma weight residual -122.60 -87.67 -34.93 0 2.50e+00 1.60e-01 1.95e+02 ... (remaining 10764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 2643 0.145 - 0.289: 6 0.289 - 0.434: 3 0.434 - 0.578: 0 0.578 - 0.723: 6 Chirality restraints: 2658 Sorted by residual: chirality pdb=" CA ALA B 106 " pdb=" N ALA B 106 " pdb=" C ALA B 106 " pdb=" CB ALA B 106 " both_signs ideal model delta sigma weight residual False 2.48 3.21 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ALA G 106 " pdb=" N ALA G 106 " pdb=" C ALA G 106 " pdb=" CB ALA G 106 " both_signs ideal model delta sigma weight residual False 2.48 3.21 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA ALA L 106 " pdb=" N ALA L 106 " pdb=" C ALA L 106 " pdb=" CB ALA L 106 " both_signs ideal model delta sigma weight residual False 2.48 3.21 -0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 2655 not shown) Planarity restraints: 2946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 28 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.86e+00 pdb=" C SER E 28 " 0.038 2.00e-02 2.50e+03 pdb=" O SER E 28 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE E 29 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER O 28 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C SER O 28 " 0.038 2.00e-02 2.50e+03 pdb=" O SER O 28 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE O 29 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER J 28 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C SER J 28 " 0.038 2.00e-02 2.50e+03 pdb=" O SER J 28 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE J 29 " -0.013 2.00e-02 2.50e+03 ... (remaining 2943 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1172 2.73 - 3.27: 16562 3.27 - 3.82: 27834 3.82 - 4.36: 30117 4.36 - 4.90: 53568 Nonbonded interactions: 129253 Sorted by model distance: nonbonded pdb=" O VAL I 29 " pdb=" OH TYR I 70 " model vdw 2.190 3.040 nonbonded pdb=" O VAL D 29 " pdb=" OH TYR D 70 " model vdw 2.190 3.040 nonbonded pdb=" O VAL N 29 " pdb=" OH TYR N 70 " model vdw 2.191 3.040 nonbonded pdb=" O SER F 41 " pdb=" NH2 ARG H 483 " model vdw 2.198 3.120 nonbonded pdb=" O SER A 41 " pdb=" NH2 ARG C 483 " model vdw 2.198 3.120 ... (remaining 129248 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'R' selection = chain 'W' selection = chain 'Y' selection = chain 'b' selection = chain 'h' selection = chain 'n' } 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: 5.020 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: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.230 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 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 : 0.003 0.089 17472 Z= 0.180 Angle : 0.790 22.257 23718 Z= 0.415 Chirality : 0.053 0.723 2658 Planarity : 0.004 0.041 2925 Dihedral : 17.503 69.387 6810 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.85 % Allowed : 32.56 % Favored : 62.59 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 10.00 % 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: -0.03 (0.19), residues: 2037 helix: 1.55 (0.21), residues: 573 sheet: 0.06 (0.25), residues: 411 loop : -0.94 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 60 TYR 0.008 0.001 TYR O 111 PHE 0.011 0.001 PHE E 68 TRP 0.014 0.001 TRP C 275 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (17409) covalent geometry : angle 0.77589 / 0.41 (23565) SS BOND : bond 0.00438 / 0.32 ( 27) SS BOND : angle 0.87926 / 0.59 ( 54) hydrogen bonds : bond 0.12422 / 8.12 ( 774) hydrogen bonds : angle 6.30080 / 4.51 ( 2061) Misc. bond : bond 0.08907 / 5.01 ( 3) link_BETA1-4 : bond 0.00630 / 0.38 ( 12) link_BETA1-4 : angle 1.88731 / 1.10 ( 36) link_NAG-ASN : bond 0.00437 / 0.29 ( 21) link_NAG-ASN : angle 2.63351 / 1.87 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 316 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 LYS cc_start: 0.8209 (mttt) cc_final: 0.8004 (mmtp) REVERT: B 158 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7724 (pp) REVERT: C 304 MET cc_start: 0.6334 (mmm) cc_final: 0.6121 (mmm) REVERT: C 406 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6210 (tmm) REVERT: C 482 ARG cc_start: 0.6238 (mtt180) cc_final: 0.5727 (mmp-170) REVERT: D 1 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: D 32 MET cc_start: 0.7481 (ttm) cc_final: 0.7136 (ttt) REVERT: E 82 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8080 (tp40) REVERT: E 109 MET cc_start: 0.7791 (mtt) cc_final: 0.7577 (mtp) REVERT: E 112 TRP cc_start: 0.7963 (m-10) cc_final: 0.6958 (m100) REVERT: G 213 CYS cc_start: 0.6541 (OUTLIER) cc_final: 0.6313 (t) REVERT: H 304 MET cc_start: 0.6370 (mmm) cc_final: 0.6104 (mmm) REVERT: H 406 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6270 (tmm) REVERT: H 482 ARG cc_start: 0.6193 (mtt180) cc_final: 0.5755 (mmp-170) REVERT: I 1 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: I 32 MET cc_start: 0.7400 (ttm) cc_final: 0.6956 (ttt) REVERT: I 104 GLU cc_start: 0.7234 (mp0) cc_final: 0.6837 (mp0) REVERT: L 229 ASP cc_start: 0.7807 (p0) cc_final: 0.7562 (p0) REVERT: M 304 MET cc_start: 0.6434 (mmm) cc_final: 0.6082 (mmm) REVERT: M 406 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.6228 (tmm) REVERT: M 482 ARG cc_start: 0.6129 (mtt180) cc_final: 0.5696 (tpm170) REVERT: N 1 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: N 32 MET cc_start: 0.7470 (ttm) cc_final: 0.7081 (ttt) REVERT: O 53 ARG cc_start: 0.7379 (ttp-170) cc_final: 0.6999 (ttp-170) outliers start: 88 outliers final: 66 residues processed: 367 average time/residue: 0.0938 time to fit residues: 56.1517 Evaluate side-chains 362 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 288 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain D residue 1 GLN Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 122 TYR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 180 SER Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 311 ASN Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 318 LEU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 390 ASP Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain H residue 429 SER Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain I residue 1 GLN Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 122 TYR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 213 CYS Chi-restraints excluded: chain L residue 226 CYS Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 299 SER Chi-restraints excluded: chain M residue 317 THR Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 390 ASP Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 429 SER Chi-restraints excluded: chain M residue 430 THR Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain O residue 74 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.0670 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN C 327 ASN C 366 HIS D 6 GLN D 91 ASN E 39 GLN E 77 ASN E 82 GLN ** G 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 GLN H 327 ASN H 366 HIS I 6 GLN I 91 ASN J 39 GLN J 77 ASN ** L 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 GLN ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 230 HIS L 244 GLN M 327 ASN M 366 HIS N 6 GLN N 91 ASN O 39 GLN O 77 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.178594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.146459 restraints weight = 24972.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.149426 restraints weight = 18058.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.151549 restraints weight = 14516.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.153059 restraints weight = 12448.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.154024 restraints weight = 11137.466| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17472 Z= 0.158 Angle : 0.661 7.487 23718 Z= 0.333 Chirality : 0.043 0.335 2658 Planarity : 0.004 0.044 2925 Dihedral : 7.804 57.324 3067 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 7.71 % Allowed : 29.42 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.04 (0.19), residues: 2037 helix: 1.57 (0.21), residues: 576 sheet: 0.14 (0.25), residues: 405 loop : -1.02 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 460 TYR 0.013 0.001 TYR L 157 PHE 0.016 0.002 PHE B 175 TRP 0.018 0.001 TRP M 275 HIS 0.004 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (17409) covalent geometry : angle 0.63664 / 0.33 (23565) SS BOND : bond 0.00868 / 0.65 ( 27) SS BOND : angle 1.04876 / 0.72 ( 54) hydrogen bonds : bond 0.04655 / 3.08 ( 774) hydrogen bonds : angle 5.46309 / 3.89 ( 2061) Misc. bond : bond 0.00223 / 0.13 ( 3) link_BETA1-4 : bond 0.00666 / 0.40 ( 12) link_BETA1-4 : angle 2.03161 / 1.23 ( 36) link_NAG-ASN : bond 0.00385 / 0.25 ( 21) link_NAG-ASN : angle 3.07109 / 2.17 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 305 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4397 (OUTLIER) cc_final: 0.4181 (mp) REVERT: B 96 LYS cc_start: 0.8347 (mttt) cc_final: 0.8103 (mmtp) REVERT: B 150 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.6961 (m-40) REVERT: B 158 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7439 (pp) REVERT: B 159 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8025 (m-30) REVERT: C 304 MET cc_start: 0.6444 (mmm) cc_final: 0.6237 (mmm) REVERT: C 406 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6178 (tmm) REVERT: D 78 GLU cc_start: 0.7425 (mp0) cc_final: 0.7111 (mp0) REVERT: D 103 LEU cc_start: 0.8725 (tt) cc_final: 0.8478 (tp) REVERT: E 60 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.7427 (m90) REVERT: F 43 LEU cc_start: 0.4321 (OUTLIER) cc_final: 0.3999 (mp) REVERT: G 150 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7049 (m-40) REVERT: G 199 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8046 (mp) REVERT: H 304 MET cc_start: 0.6428 (mmm) cc_final: 0.6215 (mmm) REVERT: H 406 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.6477 (tmm) REVERT: I 104 GLU cc_start: 0.7282 (mp0) cc_final: 0.7071 (mp0) REVERT: J 35 SER cc_start: 0.9350 (p) cc_final: 0.9074 (p) REVERT: K 43 LEU cc_start: 0.4386 (OUTLIER) cc_final: 0.4078 (mp) REVERT: L 150 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7098 (m-40) REVERT: L 199 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7699 (mp) REVERT: M 304 MET cc_start: 0.6452 (mmm) cc_final: 0.6114 (mmm) REVERT: M 406 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6298 (tmm) REVERT: O 35 SER cc_start: 0.9386 (p) cc_final: 0.9128 (p) REVERT: O 60 HIS cc_start: 0.8100 (OUTLIER) cc_final: 0.7872 (m90) REVERT: O 102 TYR cc_start: 0.8147 (m-10) cc_final: 0.7929 (m-10) outliers start: 140 outliers final: 82 residues processed: 415 average time/residue: 0.0879 time to fit residues: 60.2967 Evaluate side-chains 390 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 293 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 46 TRP Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 122 TYR Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 46 TRP Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 91 ASN Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain J residue 60 HIS Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 71 GLN Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 122 TYR Chi-restraints excluded: chain L residue 150 ASN Chi-restraints excluded: chain L residue 158 LEU Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 174 ILE Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 226 CYS Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain M residue 299 SER Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 464 LEU Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 46 TRP Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 91 ASN Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 60 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 43 optimal weight: 30.0000 chunk 48 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 177 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS C 327 ASN D 91 ASN ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 HIS H 327 ASN I 91 ASN L 71 GLN ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN O 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.178276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.146446 restraints weight = 25256.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.149644 restraints weight = 17843.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.151843 restraints weight = 14089.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.153425 restraints weight = 11966.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.154337 restraints weight = 10622.765| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17472 Z= 0.128 Angle : 0.631 9.190 23718 Z= 0.315 Chirality : 0.042 0.315 2658 Planarity : 0.004 0.043 2925 Dihedral : 6.972 58.723 2996 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 7.44 % Allowed : 29.75 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.03 (0.19), residues: 2037 helix: 1.64 (0.21), residues: 576 sheet: 0.14 (0.25), residues: 405 loop : -1.05 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 38 TYR 0.010 0.001 TYR G 157 PHE 0.016 0.001 PHE B 175 TRP 0.020 0.001 TRP H 275 HIS 0.003 0.001 HIS L 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (17409) covalent geometry : angle 0.60806 / 0.31 (23565) SS BOND : bond 0.00537 / 0.40 ( 27) SS BOND : angle 0.77518 / 0.54 ( 54) hydrogen bonds : bond 0.04366 / 2.90 ( 774) hydrogen bonds : angle 5.22775 / 3.74 ( 2061) Misc. bond : bond 0.00014 / 0.01 ( 3) link_BETA1-4 : bond 0.00708 / 0.43 ( 12) link_BETA1-4 : angle 1.97762 / 1.18 ( 36) link_NAG-ASN : bond 0.00423 / 0.28 ( 21) link_NAG-ASN : angle 2.97783 / 2.11 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 305 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4441 (OUTLIER) cc_final: 0.4170 (mp) REVERT: B 96 LYS cc_start: 0.8313 (mttt) cc_final: 0.8098 (mmtp) REVERT: B 150 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.6963 (m-40) REVERT: B 159 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: C 336 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7693 (mp) REVERT: C 406 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6194 (tmm) REVERT: E 60 HIS cc_start: 0.8090 (OUTLIER) cc_final: 0.7350 (m90) REVERT: F 43 LEU cc_start: 0.4360 (OUTLIER) cc_final: 0.4048 (mp) REVERT: G 150 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7038 (m-40) REVERT: G 199 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7985 (mp) REVERT: H 304 MET cc_start: 0.6325 (mmm) cc_final: 0.6110 (mmm) REVERT: H 406 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6501 (tmm) REVERT: I 104 GLU cc_start: 0.7353 (mp0) cc_final: 0.7090 (mp0) REVERT: K 43 LEU cc_start: 0.4331 (OUTLIER) cc_final: 0.4018 (mp) REVERT: L 150 ASN cc_start: 0.7699 (OUTLIER) cc_final: 0.7133 (m-40) REVERT: L 199 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7647 (mp) REVERT: M 304 MET cc_start: 0.6413 (mmm) cc_final: 0.6192 (mmm) REVERT: M 336 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7716 (mp) REVERT: M 406 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6277 (tmm) REVERT: O 35 SER cc_start: 0.9399 (p) cc_final: 0.9113 (p) REVERT: O 53 ARG cc_start: 0.7283 (ttp-170) cc_final: 0.7030 (ttp-170) REVERT: O 60 HIS cc_start: 0.8055 (OUTLIER) cc_final: 0.7784 (m90) outliers start: 135 outliers final: 81 residues processed: 403 average time/residue: 0.0908 time to fit residues: 60.6914 Evaluate side-chains 387 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 290 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 46 TRP Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 122 TYR Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 46 TRP Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 60 HIS Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 71 GLN Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 122 TYR Chi-restraints excluded: chain L residue 150 ASN Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 158 LEU Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 369 SER Chi-restraints excluded: chain M residue 403 ILE Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 430 THR Chi-restraints excluded: chain M residue 464 LEU Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 46 TRP Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 91 ASN Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 114 optimal weight: 0.0000 chunk 94 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 71 GLN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN E 39 GLN G 71 GLN ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 327 ASN J 39 GLN ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.176155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.144152 restraints weight = 25332.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.147203 restraints weight = 18022.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.149376 restraints weight = 14367.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.150720 restraints weight = 12267.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.151896 restraints weight = 11010.907| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17472 Z= 0.157 Angle : 0.654 7.635 23718 Z= 0.325 Chirality : 0.043 0.332 2658 Planarity : 0.004 0.042 2925 Dihedral : 6.862 58.742 2984 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 8.43 % Allowed : 28.76 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.17 (0.19), residues: 2037 helix: 1.53 (0.21), residues: 576 sheet: 0.14 (0.26), residues: 399 loop : -1.17 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 90 TYR 0.017 0.001 TYR D 31 PHE 0.017 0.002 PHE B 175 TRP 0.023 0.001 TRP M 275 HIS 0.004 0.001 HIS G 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (17409) covalent geometry : angle 0.63050 / 0.32 (23565) SS BOND : bond 0.00415 / 0.28 ( 27) SS BOND : angle 0.97300 / 0.69 ( 54) hydrogen bonds : bond 0.04511 / 2.99 ( 774) hydrogen bonds : angle 5.20577 / 3.72 ( 2061) Misc. bond : bond 0.00008 / 0.00 ( 3) link_BETA1-4 : bond 0.00647 / 0.39 ( 12) link_BETA1-4 : angle 1.98483 / 1.20 ( 36) link_NAG-ASN : bond 0.00352 / 0.23 ( 21) link_NAG-ASN : angle 3.06407 / 2.18 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 291 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4465 (OUTLIER) cc_final: 0.4181 (mp) REVERT: B 150 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.6967 (m-40) REVERT: B 159 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8068 (m-30) REVERT: C 336 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7704 (mp) REVERT: C 406 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6154 (tmm) REVERT: E 60 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7373 (m90) REVERT: F 43 LEU cc_start: 0.4301 (OUTLIER) cc_final: 0.4011 (mp) REVERT: G 150 ASN cc_start: 0.7874 (OUTLIER) cc_final: 0.7212 (m-40) REVERT: G 199 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8018 (mp) REVERT: H 336 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7647 (mp) REVERT: H 406 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6486 (tmm) REVERT: I 104 GLU cc_start: 0.7374 (mp0) cc_final: 0.7141 (mp0) REVERT: K 43 LEU cc_start: 0.4381 (OUTLIER) cc_final: 0.4102 (mp) REVERT: L 150 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7212 (m-40) REVERT: L 199 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7748 (mp) REVERT: M 304 MET cc_start: 0.6429 (mmm) cc_final: 0.6141 (mmm) REVERT: M 336 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7750 (mp) REVERT: M 406 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6296 (tmm) REVERT: N 81 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.7112 (t0) REVERT: O 35 SER cc_start: 0.9472 (p) cc_final: 0.9189 (p) REVERT: O 60 HIS cc_start: 0.8077 (OUTLIER) cc_final: 0.7802 (m90) outliers start: 153 outliers final: 106 residues processed: 392 average time/residue: 0.0853 time to fit residues: 55.8812 Evaluate side-chains 410 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 286 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 46 TRP Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 122 TYR Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 311 ASN Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain H residue 464 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 46 TRP Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 60 HIS Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 71 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 122 TYR Chi-restraints excluded: chain L residue 132 MET Chi-restraints excluded: chain L residue 150 ASN Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 226 CYS Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 403 ILE Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 430 THR Chi-restraints excluded: chain M residue 464 LEU Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 46 TRP Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 89 GLU Chi-restraints excluded: chain O residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 65 optimal weight: 3.9990 chunk 144 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 60.6315 > 50:) chunk 24 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 86 optimal weight: 0.0670 chunk 48 optimal weight: 0.0060 overall best weight: 1.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 71 GLN D 91 ASN ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 GLN ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.173776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.141891 restraints weight = 25228.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.144882 restraints weight = 18066.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.146947 restraints weight = 14440.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.148419 restraints weight = 12402.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.149294 restraints weight = 11107.681| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17472 Z= 0.191 Angle : 0.690 7.225 23718 Z= 0.343 Chirality : 0.044 0.350 2658 Planarity : 0.004 0.039 2925 Dihedral : 7.102 56.622 2984 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 9.86 % Allowed : 27.66 % Favored : 62.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.34 (0.19), residues: 2037 helix: 1.35 (0.21), residues: 576 sheet: 0.11 (0.26), residues: 399 loop : -1.29 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 60 TYR 0.017 0.002 TYR I 31 PHE 0.019 0.002 PHE L 70 TRP 0.026 0.002 TRP C 275 HIS 0.006 0.001 HIS L 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (17409) covalent geometry : angle 0.66448 / 0.34 (23565) SS BOND : bond 0.00591 / 0.42 ( 27) SS BOND : angle 1.24552 / 0.88 ( 54) hydrogen bonds : bond 0.04849 / 3.21 ( 774) hydrogen bonds : angle 5.31782 / 3.79 ( 2061) Misc. bond : bond 0.00037 / 0.02 ( 3) link_BETA1-4 : bond 0.00642 / 0.39 ( 12) link_BETA1-4 : angle 1.99463 / 1.22 ( 36) link_NAG-ASN : bond 0.00326 / 0.21 ( 21) link_NAG-ASN : angle 3.21337 / 2.29 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 293 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4500 (OUTLIER) cc_final: 0.4267 (mp) REVERT: B 159 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8117 (m-30) REVERT: B 213 CYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6802 (t) REVERT: C 406 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6215 (tmm) REVERT: E 60 HIS cc_start: 0.8166 (OUTLIER) cc_final: 0.7406 (m90) REVERT: F 43 LEU cc_start: 0.4424 (OUTLIER) cc_final: 0.4116 (mp) REVERT: G 150 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7362 (m110) REVERT: G 199 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8109 (mp) REVERT: G 213 CYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6648 (t) REVERT: H 336 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7806 (mp) REVERT: H 406 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6480 (tmm) REVERT: K 43 LEU cc_start: 0.4409 (OUTLIER) cc_final: 0.4123 (mp) REVERT: L 150 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7293 (m-40) REVERT: L 199 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7887 (mp) REVERT: M 304 MET cc_start: 0.6479 (mmm) cc_final: 0.6206 (mmm) REVERT: M 336 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7868 (mp) REVERT: M 406 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6302 (tmm) REVERT: N 32 MET cc_start: 0.7721 (ttm) cc_final: 0.7470 (ttm) REVERT: O 35 SER cc_start: 0.9524 (p) cc_final: 0.9264 (p) REVERT: O 60 HIS cc_start: 0.8145 (OUTLIER) cc_final: 0.7845 (m90) outliers start: 179 outliers final: 124 residues processed: 412 average time/residue: 0.0898 time to fit residues: 60.6888 Evaluate side-chains 421 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 280 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 46 TRP Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 122 TYR Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain H residue 390 ASP Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain H residue 460 ARG Chi-restraints excluded: chain H residue 464 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 32 MET Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 46 TRP Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 60 HIS Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 71 GLN Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 111 SER Chi-restraints excluded: chain L residue 122 TYR Chi-restraints excluded: chain L residue 150 ASN Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 226 CYS Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 390 ASP Chi-restraints excluded: chain M residue 403 ILE Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 430 THR Chi-restraints excluded: chain M residue 460 ARG Chi-restraints excluded: chain M residue 464 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 46 TRP Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 89 GLU Chi-restraints excluded: chain O residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 81 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 184 optimal weight: 0.0030 chunk 79 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN G 71 GLN ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 HIS ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.177241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.145536 restraints weight = 25131.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.148665 restraints weight = 17793.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.150856 restraints weight = 14102.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.152405 restraints weight = 11978.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.153155 restraints weight = 10664.067| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17472 Z= 0.120 Angle : 0.636 8.263 23718 Z= 0.314 Chirality : 0.042 0.314 2658 Planarity : 0.004 0.041 2925 Dihedral : 6.927 55.940 2984 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 7.55 % Allowed : 29.64 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.18 (0.19), residues: 2037 helix: 1.59 (0.21), residues: 576 sheet: 0.16 (0.26), residues: 399 loop : -1.23 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 90 TYR 0.012 0.001 TYR D 31 PHE 0.015 0.001 PHE B 175 TRP 0.027 0.001 TRP C 275 HIS 0.003 0.001 HIS L 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (17409) covalent geometry : angle 0.61185 / 0.31 (23565) SS BOND : bond 0.00677 / 0.49 ( 27) SS BOND : angle 0.94405 / 0.68 ( 54) hydrogen bonds : bond 0.04186 / 2.77 ( 774) hydrogen bonds : angle 5.07299 / 3.61 ( 2061) Misc. bond : bond 0.00028 / 0.02 ( 3) link_BETA1-4 : bond 0.00688 / 0.41 ( 12) link_BETA1-4 : angle 1.98319 / 1.18 ( 36) link_NAG-ASN : bond 0.00444 / 0.29 ( 21) link_NAG-ASN : angle 3.01381 / 2.14 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 290 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4447 (OUTLIER) cc_final: 0.4189 (mp) REVERT: B 158 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7334 (pp) REVERT: B 159 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8106 (m-30) REVERT: C 406 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6225 (tmm) REVERT: E 60 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.7366 (m90) REVERT: F 43 LEU cc_start: 0.4201 (OUTLIER) cc_final: 0.3946 (mp) REVERT: G 150 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7277 (m-40) REVERT: G 199 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7993 (mp) REVERT: G 213 CYS cc_start: 0.6841 (OUTLIER) cc_final: 0.6606 (t) REVERT: H 336 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7695 (mp) REVERT: H 406 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6485 (tmm) REVERT: K 43 LEU cc_start: 0.4270 (OUTLIER) cc_final: 0.4004 (mp) REVERT: L 150 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7247 (m-40) REVERT: L 199 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7699 (mp) REVERT: M 304 MET cc_start: 0.6387 (mmm) cc_final: 0.6135 (mmm) REVERT: M 329 MET cc_start: 0.7349 (ppp) cc_final: 0.6840 (ppp) REVERT: M 336 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7746 (mp) REVERT: M 406 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6334 (tmm) REVERT: O 35 SER cc_start: 0.9480 (p) cc_final: 0.9207 (p) REVERT: O 60 HIS cc_start: 0.8106 (OUTLIER) cc_final: 0.7846 (m90) outliers start: 137 outliers final: 82 residues processed: 388 average time/residue: 0.0945 time to fit residues: 60.7365 Evaluate side-chains 377 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 278 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 46 TRP Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 122 TYR Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 46 TRP Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 71 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 122 TYR Chi-restraints excluded: chain L residue 150 ASN Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 226 CYS Chi-restraints excluded: chain M residue 299 SER Chi-restraints excluded: chain M residue 333 ILE Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 403 ILE Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 464 LEU Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 34 MET Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 89 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 47 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 136 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 182 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN G 98 HIS ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.175574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.144163 restraints weight = 24861.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.147209 restraints weight = 17658.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149313 restraints weight = 14011.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.150817 restraints weight = 11954.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.151889 restraints weight = 10638.084| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17472 Z= 0.133 Angle : 0.662 9.473 23718 Z= 0.324 Chirality : 0.043 0.325 2658 Planarity : 0.004 0.040 2925 Dihedral : 6.883 55.300 2984 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 7.22 % Allowed : 30.41 % Favored : 62.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.17 (0.19), residues: 2037 helix: 1.59 (0.21), residues: 576 sheet: 0.19 (0.25), residues: 399 loop : -1.23 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 460 TYR 0.013 0.001 TYR N 31 PHE 0.018 0.001 PHE G 175 TRP 0.029 0.001 TRP C 275 HIS 0.003 0.001 HIS M 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (17409) covalent geometry : angle 0.63948 / 0.32 (23565) SS BOND : bond 0.00461 / 0.33 ( 27) SS BOND : angle 0.96719 / 0.70 ( 54) hydrogen bonds : bond 0.04254 / 2.81 ( 774) hydrogen bonds : angle 5.04485 / 3.59 ( 2061) Misc. bond : bond 0.00033 / 0.02 ( 3) link_BETA1-4 : bond 0.00670 / 0.40 ( 12) link_BETA1-4 : angle 1.98821 / 1.19 ( 36) link_NAG-ASN : bond 0.00415 / 0.27 ( 21) link_NAG-ASN : angle 3.01082 / 2.13 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 279 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4462 (OUTLIER) cc_final: 0.4219 (mp) REVERT: B 158 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7309 (pp) REVERT: B 159 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8117 (m-30) REVERT: C 406 MET cc_start: 0.6978 (ttp) cc_final: 0.6231 (tmm) REVERT: C 462 ASN cc_start: 0.6310 (OUTLIER) cc_final: 0.6032 (p0) REVERT: E 59 TYR cc_start: 0.8189 (t80) cc_final: 0.7755 (t80) REVERT: E 60 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7375 (m90) REVERT: F 43 LEU cc_start: 0.4262 (OUTLIER) cc_final: 0.4004 (mp) REVERT: G 150 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7367 (m110) REVERT: G 199 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8026 (mp) REVERT: G 213 CYS cc_start: 0.6841 (OUTLIER) cc_final: 0.6600 (t) REVERT: H 336 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7686 (mp) REVERT: H 406 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6512 (tmm) REVERT: H 462 ASN cc_start: 0.6374 (OUTLIER) cc_final: 0.6076 (p0) REVERT: K 43 LEU cc_start: 0.4342 (OUTLIER) cc_final: 0.4064 (mp) REVERT: L 150 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7269 (m-40) REVERT: L 199 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7723 (mp) REVERT: M 304 MET cc_start: 0.6439 (mmm) cc_final: 0.6124 (mmm) REVERT: M 329 MET cc_start: 0.7389 (ppp) cc_final: 0.6911 (ppp) REVERT: M 336 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7779 (mp) REVERT: M 406 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6339 (tmm) REVERT: O 35 SER cc_start: 0.9509 (p) cc_final: 0.9247 (p) REVERT: O 60 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7845 (m90) outliers start: 131 outliers final: 100 residues processed: 368 average time/residue: 0.0892 time to fit residues: 54.6983 Evaluate side-chains 391 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 273 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 122 TYR Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain H residue 462 ASN Chi-restraints excluded: chain H residue 464 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 46 TRP Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 60 HIS Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 122 TYR Chi-restraints excluded: chain L residue 150 ASN Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 226 CYS Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 299 SER Chi-restraints excluded: chain M residue 333 ILE Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 388 ILE Chi-restraints excluded: chain M residue 390 ASP Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 464 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 34 MET Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 89 GLU Chi-restraints excluded: chain O residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 45 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 71 GLN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 GLN L 71 GLN ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.175883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.144185 restraints weight = 25213.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.147316 restraints weight = 17766.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149481 restraints weight = 14033.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.151015 restraints weight = 11920.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.151957 restraints weight = 10617.358| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17472 Z= 0.124 Angle : 0.643 7.238 23718 Z= 0.317 Chirality : 0.042 0.320 2658 Planarity : 0.004 0.039 2925 Dihedral : 6.750 55.923 2981 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 7.16 % Allowed : 30.58 % Favored : 62.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.12 (0.19), residues: 2037 helix: 1.66 (0.21), residues: 576 sheet: 0.22 (0.25), residues: 399 loop : -1.22 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 460 TYR 0.012 0.001 TYR N 31 PHE 0.018 0.001 PHE G 175 TRP 0.032 0.001 TRP C 275 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (17409) covalent geometry : angle 0.62051 / 0.31 (23565) SS BOND : bond 0.00460 / 0.33 ( 27) SS BOND : angle 0.90068 / 0.65 ( 54) hydrogen bonds : bond 0.04163 / 2.75 ( 774) hydrogen bonds : angle 4.97713 / 3.55 ( 2061) Misc. bond : bond 0.00033 / 0.02 ( 3) link_BETA1-4 : bond 0.00685 / 0.42 ( 12) link_BETA1-4 : angle 1.96557 / 1.17 ( 36) link_NAG-ASN : bond 0.00421 / 0.28 ( 21) link_NAG-ASN : angle 2.97346 / 2.11 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 278 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4425 (OUTLIER) cc_final: 0.4175 (mp) REVERT: B 158 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7308 (pp) REVERT: B 159 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8123 (m-30) REVERT: C 352 SER cc_start: 0.7977 (OUTLIER) cc_final: 0.7266 (p) REVERT: C 406 MET cc_start: 0.6944 (ttp) cc_final: 0.6241 (tmm) REVERT: C 462 ASN cc_start: 0.6367 (OUTLIER) cc_final: 0.6084 (p0) REVERT: E 59 TYR cc_start: 0.8166 (t80) cc_final: 0.7669 (t80) REVERT: E 60 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7378 (m90) REVERT: F 43 LEU cc_start: 0.4165 (OUTLIER) cc_final: 0.3873 (mp) REVERT: G 150 ASN cc_start: 0.7939 (OUTLIER) cc_final: 0.7285 (m-40) REVERT: G 199 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7987 (mp) REVERT: G 213 CYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6579 (t) REVERT: H 336 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7741 (mp) REVERT: H 352 SER cc_start: 0.7793 (OUTLIER) cc_final: 0.7192 (p) REVERT: H 406 MET cc_start: 0.6951 (ttp) cc_final: 0.6539 (tmm) REVERT: H 462 ASN cc_start: 0.6366 (OUTLIER) cc_final: 0.6143 (p0) REVERT: K 43 LEU cc_start: 0.4310 (OUTLIER) cc_final: 0.4032 (mp) REVERT: L 150 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7323 (m-40) REVERT: L 199 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7703 (mp) REVERT: M 304 MET cc_start: 0.6428 (mmm) cc_final: 0.6102 (mmm) REVERT: M 329 MET cc_start: 0.7435 (ppp) cc_final: 0.6941 (ppp) REVERT: M 336 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7835 (mp) REVERT: M 406 MET cc_start: 0.6969 (ttp) cc_final: 0.6324 (tmm) REVERT: M 462 ASN cc_start: 0.6275 (OUTLIER) cc_final: 0.5980 (p0) REVERT: O 35 SER cc_start: 0.9499 (p) cc_final: 0.9233 (p) REVERT: O 60 HIS cc_start: 0.8069 (OUTLIER) cc_final: 0.7760 (m90) outliers start: 130 outliers final: 98 residues processed: 370 average time/residue: 0.0840 time to fit residues: 52.3808 Evaluate side-chains 388 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 271 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 122 TYR Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain H residue 430 THR Chi-restraints excluded: chain H residue 462 ASN Chi-restraints excluded: chain H residue 464 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 60 HIS Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 71 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 122 TYR Chi-restraints excluded: chain L residue 150 ASN Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 226 CYS Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 299 SER Chi-restraints excluded: chain M residue 333 ILE Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 388 ILE Chi-restraints excluded: chain M residue 430 THR Chi-restraints excluded: chain M residue 462 ASN Chi-restraints excluded: chain M residue 464 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 34 MET Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 74 ASN Chi-restraints excluded: chain O residue 89 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 81 optimal weight: 0.0060 chunk 15 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 136 optimal weight: 0.0870 chunk 117 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.4974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 71 GLN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 GLN ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.177584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.146146 restraints weight = 24973.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.149285 restraints weight = 17573.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.151483 restraints weight = 13873.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.153034 restraints weight = 11750.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.154070 restraints weight = 10430.151| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17472 Z= 0.111 Angle : 0.632 7.278 23718 Z= 0.310 Chirality : 0.042 0.306 2658 Planarity : 0.004 0.037 2925 Dihedral : 6.470 57.049 2975 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 6.45 % Allowed : 31.13 % Favored : 62.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.01 (0.19), residues: 2037 helix: 1.82 (0.21), residues: 576 sheet: 0.27 (0.25), residues: 399 loop : -1.19 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 460 TYR 0.011 0.001 TYR N 31 PHE 0.017 0.001 PHE G 175 TRP 0.034 0.001 TRP C 275 HIS 0.002 0.001 HIS L 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (17409) covalent geometry : angle 0.60947 / 0.31 (23565) SS BOND : bond 0.00351 / 0.26 ( 27) SS BOND : angle 0.86161 / 0.63 ( 54) hydrogen bonds : bond 0.03965 / 2.63 ( 774) hydrogen bonds : angle 4.87517 / 3.48 ( 2061) Misc. bond : bond 0.00031 / 0.02 ( 3) link_BETA1-4 : bond 0.00690 / 0.42 ( 12) link_BETA1-4 : angle 1.95815 / 1.15 ( 36) link_NAG-ASN : bond 0.00464 / 0.31 ( 21) link_NAG-ASN : angle 2.89581 / 2.04 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 287 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4388 (OUTLIER) cc_final: 0.4134 (mp) REVERT: B 158 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7358 (pp) REVERT: B 159 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: C 329 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6643 (ppp) REVERT: C 352 SER cc_start: 0.7902 (t) cc_final: 0.7195 (p) REVERT: C 406 MET cc_start: 0.6967 (ttp) cc_final: 0.6298 (tmm) REVERT: C 462 ASN cc_start: 0.6272 (OUTLIER) cc_final: 0.5977 (p0) REVERT: E 60 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7293 (m90) REVERT: F 43 LEU cc_start: 0.4142 (OUTLIER) cc_final: 0.3851 (mp) REVERT: G 134 TRP cc_start: 0.7583 (m100) cc_final: 0.7080 (m100) REVERT: G 150 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7264 (m-40) REVERT: G 199 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7930 (mp) REVERT: G 213 CYS cc_start: 0.6767 (OUTLIER) cc_final: 0.6537 (t) REVERT: H 336 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7733 (mp) REVERT: H 352 SER cc_start: 0.7745 (OUTLIER) cc_final: 0.7202 (p) REVERT: H 406 MET cc_start: 0.6978 (ttp) cc_final: 0.6599 (tmm) REVERT: H 462 ASN cc_start: 0.6308 (OUTLIER) cc_final: 0.6044 (p0) REVERT: K 43 LEU cc_start: 0.4318 (OUTLIER) cc_final: 0.4067 (mp) REVERT: L 150 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7302 (m-40) REVERT: L 199 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7659 (mp) REVERT: M 304 MET cc_start: 0.6377 (mmm) cc_final: 0.6050 (mmm) REVERT: M 329 MET cc_start: 0.7329 (ppp) cc_final: 0.6909 (ppp) REVERT: M 336 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7812 (mp) REVERT: M 352 SER cc_start: 0.7801 (OUTLIER) cc_final: 0.7254 (p) REVERT: M 406 MET cc_start: 0.6929 (ttp) cc_final: 0.6345 (tmm) REVERT: M 462 ASN cc_start: 0.6189 (OUTLIER) cc_final: 0.5920 (p0) REVERT: O 35 SER cc_start: 0.9499 (p) cc_final: 0.9270 (p) REVERT: O 60 HIS cc_start: 0.8033 (OUTLIER) cc_final: 0.7753 (m90) outliers start: 117 outliers final: 81 residues processed: 375 average time/residue: 0.0857 time to fit residues: 53.9014 Evaluate side-chains 384 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 283 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 122 TYR Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain H residue 462 ASN Chi-restraints excluded: chain H residue 464 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 71 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 122 TYR Chi-restraints excluded: chain L residue 150 ASN Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 226 CYS Chi-restraints excluded: chain M residue 299 SER Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 388 ILE Chi-restraints excluded: chain M residue 390 ASP Chi-restraints excluded: chain M residue 462 ASN Chi-restraints excluded: chain M residue 464 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 89 GLU Chi-restraints excluded: chain O residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 106 optimal weight: 0.5980 chunk 170 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 71 GLN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN ** G 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.176675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.145208 restraints weight = 24920.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.148351 restraints weight = 17581.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.150505 restraints weight = 13898.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.151994 restraints weight = 11808.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.152903 restraints weight = 10529.328| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17472 Z= 0.125 Angle : 0.645 9.366 23718 Z= 0.316 Chirality : 0.042 0.315 2658 Planarity : 0.004 0.037 2925 Dihedral : 6.456 57.789 2975 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 6.06 % Allowed : 31.57 % Favored : 62.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.03 (0.19), residues: 2037 helix: 1.79 (0.21), residues: 576 sheet: 0.27 (0.26), residues: 399 loop : -1.21 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 460 TYR 0.013 0.001 TYR H 363 PHE 0.018 0.001 PHE G 175 TRP 0.035 0.001 TRP C 275 HIS 0.005 0.001 HIS G 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (17409) covalent geometry : angle 0.62340 / 0.31 (23565) SS BOND : bond 0.00453 / 0.33 ( 27) SS BOND : angle 0.99087 / 0.72 ( 54) hydrogen bonds : bond 0.04083 / 2.70 ( 774) hydrogen bonds : angle 4.88414 / 3.48 ( 2061) Misc. bond : bond 0.00035 / 0.02 ( 3) link_BETA1-4 : bond 0.00646 / 0.39 ( 12) link_BETA1-4 : angle 1.94434 / 1.15 ( 36) link_NAG-ASN : bond 0.00410 / 0.27 ( 21) link_NAG-ASN : angle 2.90322 / 2.05 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 288 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.4416 (OUTLIER) cc_final: 0.4161 (mp) REVERT: B 158 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7311 (pp) REVERT: B 159 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: C 329 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6671 (ppp) REVERT: C 352 SER cc_start: 0.7887 (t) cc_final: 0.7185 (p) REVERT: C 406 MET cc_start: 0.6958 (ttp) cc_final: 0.6319 (tmm) REVERT: C 462 ASN cc_start: 0.6335 (OUTLIER) cc_final: 0.6049 (p0) REVERT: E 60 HIS cc_start: 0.8031 (OUTLIER) cc_final: 0.7317 (m90) REVERT: F 43 LEU cc_start: 0.4134 (OUTLIER) cc_final: 0.3833 (mp) REVERT: G 134 TRP cc_start: 0.7563 (m100) cc_final: 0.7090 (m100) REVERT: G 150 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7291 (m-40) REVERT: G 199 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7962 (mp) REVERT: G 213 CYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6556 (t) REVERT: H 336 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7762 (mp) REVERT: H 352 SER cc_start: 0.7662 (OUTLIER) cc_final: 0.7147 (p) REVERT: H 406 MET cc_start: 0.6981 (ttp) cc_final: 0.6634 (tmm) REVERT: H 462 ASN cc_start: 0.6167 (OUTLIER) cc_final: 0.5951 (p0) REVERT: J 112 TRP cc_start: 0.7907 (m-10) cc_final: 0.7013 (m100) REVERT: K 43 LEU cc_start: 0.4381 (OUTLIER) cc_final: 0.4095 (mp) REVERT: L 150 ASN cc_start: 0.7775 (OUTLIER) cc_final: 0.7394 (m-40) REVERT: L 199 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7695 (mp) REVERT: M 304 MET cc_start: 0.6448 (mmm) cc_final: 0.6181 (mmm) REVERT: M 329 MET cc_start: 0.7322 (ppp) cc_final: 0.6921 (ppp) REVERT: M 336 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7827 (mp) REVERT: M 352 SER cc_start: 0.7846 (OUTLIER) cc_final: 0.7298 (p) REVERT: M 406 MET cc_start: 0.6955 (ttp) cc_final: 0.6378 (tmm) REVERT: M 462 ASN cc_start: 0.6263 (OUTLIER) cc_final: 0.6057 (p0) REVERT: O 60 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7745 (m90) outliers start: 110 outliers final: 87 residues processed: 371 average time/residue: 0.0850 time to fit residues: 52.5330 Evaluate side-chains 385 residues out of total 1818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 278 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 122 TYR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 122 TYR Chi-restraints excluded: chain G residue 150 ASN Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 299 SER Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain H residue 462 ASN Chi-restraints excluded: chain H residue 464 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 60 HIS Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 122 TYR Chi-restraints excluded: chain L residue 132 MET Chi-restraints excluded: chain L residue 150 ASN Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 166 ASN Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 226 CYS Chi-restraints excluded: chain M residue 299 SER Chi-restraints excluded: chain M residue 333 ILE Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 388 ILE Chi-restraints excluded: chain M residue 390 ASP Chi-restraints excluded: chain M residue 430 THR Chi-restraints excluded: chain M residue 462 ASN Chi-restraints excluded: chain M residue 464 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 60 HIS Chi-restraints excluded: chain O residue 89 GLU Chi-restraints excluded: chain O residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 153 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 122 optimal weight: 0.0770 chunk 192 optimal weight: 0.2980 chunk 193 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 132 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 71 GLN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN ** G 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.178013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.146466 restraints weight = 25060.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.149667 restraints weight = 17559.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.151842 restraints weight = 13822.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.153170 restraints weight = 11720.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.154416 restraints weight = 10466.858| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17472 Z= 0.119 Angle : 0.644 9.087 23718 Z= 0.315 Chirality : 0.042 0.312 2658 Planarity : 0.004 0.038 2925 Dihedral : 6.435 58.386 2975 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 6.61 % Allowed : 30.96 % Favored : 62.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.02 (0.19), residues: 2037 helix: 1.84 (0.21), residues: 576 sheet: 0.27 (0.26), residues: 399 loop : -1.22 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 460 TYR 0.008 0.001 TYR L 157 PHE 0.017 0.001 PHE G 175 TRP 0.035 0.001 TRP C 275 HIS 0.006 0.001 HIS L 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (17409) covalent geometry : angle 0.62258 / 0.31 (23565) SS BOND : bond 0.00419 / 0.30 ( 27) SS BOND : angle 0.92711 / 0.68 ( 54) hydrogen bonds : bond 0.04015 / 2.65 ( 774) hydrogen bonds : angle 4.85246 / 3.46 ( 2061) Misc. bond : bond 0.00035 / 0.02 ( 3) link_BETA1-4 : bond 0.00665 / 0.40 ( 12) link_BETA1-4 : angle 1.93141 / 1.14 ( 36) link_NAG-ASN : bond 0.00429 / 0.29 ( 21) link_NAG-ASN : angle 2.89972 / 2.06 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2570.02 seconds wall clock time: 45 minutes 17.59 seconds (2717.59 seconds total)