Starting phenix.real_space_refine on Sat Mar 7 04:01:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7boy_30136/03_2026/7boy_30136.cif Found real_map, /net/cci-nas-00/data/ceres_data/7boy_30136/03_2026/7boy_30136.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/7boy_30136/03_2026/7boy_30136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7boy_30136/03_2026/7boy_30136.map" model { file = "/net/cci-nas-00/data/ceres_data/7boy_30136/03_2026/7boy_30136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7boy_30136/03_2026/7boy_30136.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= 0.035 sd= 0.651 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 90 5.16 5 C 23970 2.51 5 N 6504 2.21 5 O 7230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37794 Number of models: 1 Model: "" Number of chains: 6 Chain: "s" Number of atoms: 6299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6299 Classifications: {'peptide': 790} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 743} Chain breaks: 1 Chain: "t" Number of atoms: 6299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6299 Classifications: {'peptide': 790} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 743} Chain breaks: 1 Chain: "u" Number of atoms: 6299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6299 Classifications: {'peptide': 790} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 743} Chain breaks: 1 Chain: "v" Number of atoms: 6299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6299 Classifications: {'peptide': 790} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 743} Chain breaks: 1 Chain: "w" Number of atoms: 6299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6299 Classifications: {'peptide': 790} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 743} Chain breaks: 1 Chain: "x" Number of atoms: 6299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6299 Classifications: {'peptide': 790} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 743} Chain breaks: 1 Time building chain proxies: 7.75, per 1000 atoms: 0.21 Number of scatterers: 37794 At special positions: 0 Unit cell: (161.29, 176.53, 160.02, 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 90 16.00 O 7230 8.00 N 6504 7.00 C 23970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.7 seconds 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8760 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 114 sheets defined 5.3% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 's' and resid 111 through 115 Processing helix chain 's' and resid 168 through 172 removed outlier: 3.503A pdb=" N GLY s 171 " --> pdb=" O HIS s 168 " (cutoff:3.500A) Processing helix chain 's' and resid 184 through 189 removed outlier: 4.114A pdb=" N ASN s 189 " --> pdb=" O PRO s 185 " (cutoff:3.500A) Processing helix chain 's' and resid 192 through 207 removed outlier: 4.084A pdb=" N LEU s 196 " --> pdb=" O ASP s 192 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU s 198 " --> pdb=" O GLN s 194 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA s 201 " --> pdb=" O ALA s 197 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN s 203 " --> pdb=" O GLU s 199 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET s 204 " --> pdb=" O LEU s 200 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR s 206 " --> pdb=" O LYS s 202 " (cutoff:3.500A) Processing helix chain 's' and resid 617 through 621 Processing helix chain 's' and resid 662 through 666 removed outlier: 3.728A pdb=" N ARG s 665 " --> pdb=" O LEU s 662 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N MET s 666 " --> pdb=" O GLU s 663 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 662 through 666' Processing helix chain 't' and resid 111 through 115 Processing helix chain 't' and resid 168 through 172 removed outlier: 3.502A pdb=" N GLY t 171 " --> pdb=" O HIS t 168 " (cutoff:3.500A) Processing helix chain 't' and resid 184 through 189 removed outlier: 4.112A pdb=" N ASN t 189 " --> pdb=" O PRO t 185 " (cutoff:3.500A) Processing helix chain 't' and resid 192 through 207 removed outlier: 4.083A pdb=" N LEU t 196 " --> pdb=" O ASP t 192 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU t 198 " --> pdb=" O GLN t 194 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA t 201 " --> pdb=" O ALA t 197 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN t 203 " --> pdb=" O GLU t 199 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET t 204 " --> pdb=" O LEU t 200 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR t 206 " --> pdb=" O LYS t 202 " (cutoff:3.500A) Processing helix chain 't' and resid 617 through 621 Processing helix chain 't' and resid 662 through 666 removed outlier: 3.729A pdb=" N ARG t 665 " --> pdb=" O LEU t 662 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N MET t 666 " --> pdb=" O GLU t 663 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 662 through 666' Processing helix chain 'u' and resid 111 through 115 Processing helix chain 'u' and resid 168 through 172 removed outlier: 3.503A pdb=" N GLY u 171 " --> pdb=" O HIS u 168 " (cutoff:3.500A) Processing helix chain 'u' and resid 184 through 189 removed outlier: 4.113A pdb=" N ASN u 189 " --> pdb=" O PRO u 185 " (cutoff:3.500A) Processing helix chain 'u' and resid 192 through 207 removed outlier: 4.084A pdb=" N LEU u 196 " --> pdb=" O ASP u 192 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU u 198 " --> pdb=" O GLN u 194 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA u 201 " --> pdb=" O ALA u 197 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN u 203 " --> pdb=" O GLU u 199 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET u 204 " --> pdb=" O LEU u 200 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR u 206 " --> pdb=" O LYS u 202 " (cutoff:3.500A) Processing helix chain 'u' and resid 617 through 621 Processing helix chain 'u' and resid 662 through 666 removed outlier: 3.729A pdb=" N ARG u 665 " --> pdb=" O LEU u 662 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N MET u 666 " --> pdb=" O GLU u 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 662 through 666' Processing helix chain 'v' and resid 111 through 115 Processing helix chain 'v' and resid 168 through 172 removed outlier: 3.502A pdb=" N GLY v 171 " --> pdb=" O HIS v 168 " (cutoff:3.500A) Processing helix chain 'v' and resid 184 through 189 removed outlier: 4.112A pdb=" N ASN v 189 " --> pdb=" O PRO v 185 " (cutoff:3.500A) Processing helix chain 'v' and resid 192 through 207 removed outlier: 4.084A pdb=" N LEU v 196 " --> pdb=" O ASP v 192 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU v 198 " --> pdb=" O GLN v 194 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA v 201 " --> pdb=" O ALA v 197 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN v 203 " --> pdb=" O GLU v 199 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET v 204 " --> pdb=" O LEU v 200 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR v 206 " --> pdb=" O LYS v 202 " (cutoff:3.500A) Processing helix chain 'v' and resid 617 through 621 Processing helix chain 'v' and resid 662 through 666 removed outlier: 3.729A pdb=" N ARG v 665 " --> pdb=" O LEU v 662 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N MET v 666 " --> pdb=" O GLU v 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 662 through 666' Processing helix chain 'w' and resid 111 through 115 Processing helix chain 'w' and resid 168 through 172 removed outlier: 3.502A pdb=" N GLY w 171 " --> pdb=" O HIS w 168 " (cutoff:3.500A) Processing helix chain 'w' and resid 184 through 189 removed outlier: 4.113A pdb=" N ASN w 189 " --> pdb=" O PRO w 185 " (cutoff:3.500A) Processing helix chain 'w' and resid 192 through 207 removed outlier: 4.082A pdb=" N LEU w 196 " --> pdb=" O ASP w 192 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU w 198 " --> pdb=" O GLN w 194 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA w 201 " --> pdb=" O ALA w 197 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN w 203 " --> pdb=" O GLU w 199 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET w 204 " --> pdb=" O LEU w 200 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR w 206 " --> pdb=" O LYS w 202 " (cutoff:3.500A) Processing helix chain 'w' and resid 617 through 621 Processing helix chain 'w' and resid 662 through 666 removed outlier: 3.728A pdb=" N ARG w 665 " --> pdb=" O LEU w 662 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N MET w 666 " --> pdb=" O GLU w 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 662 through 666' Processing helix chain 'x' and resid 111 through 115 Processing helix chain 'x' and resid 168 through 172 removed outlier: 3.501A pdb=" N GLY x 171 " --> pdb=" O HIS x 168 " (cutoff:3.500A) Processing helix chain 'x' and resid 184 through 189 removed outlier: 4.114A pdb=" N ASN x 189 " --> pdb=" O PRO x 185 " (cutoff:3.500A) Processing helix chain 'x' and resid 192 through 207 removed outlier: 4.084A pdb=" N LEU x 196 " --> pdb=" O ASP x 192 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU x 198 " --> pdb=" O GLN x 194 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA x 201 " --> pdb=" O ALA x 197 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN x 203 " --> pdb=" O GLU x 199 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET x 204 " --> pdb=" O LEU x 200 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR x 206 " --> pdb=" O LYS x 202 " (cutoff:3.500A) Processing helix chain 'x' and resid 617 through 621 Processing helix chain 'x' and resid 662 through 666 removed outlier: 3.729A pdb=" N ARG x 665 " --> pdb=" O LEU x 662 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N MET x 666 " --> pdb=" O GLU x 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 662 through 666' Processing sheet with id=AA1, first strand: chain 's' and resid 4 through 8 removed outlier: 3.840A pdb=" N GLY s 780 " --> pdb=" O ASN s 709 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU s 784 " --> pdb=" O ARG s 705 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG s 705 " --> pdb=" O GLU s 784 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN s 786 " --> pdb=" O LEU s 703 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU s 703 " --> pdb=" O ASN s 786 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU s 788 " --> pdb=" O LEU s 701 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU s 701 " --> pdb=" O LEU s 788 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 's' and resid 4 through 8 removed outlier: 3.840A pdb=" N GLY s 780 " --> pdb=" O ASN s 709 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU s 784 " --> pdb=" O ARG s 705 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG s 705 " --> pdb=" O GLU s 784 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN s 786 " --> pdb=" O LEU s 703 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU s 703 " --> pdb=" O ASN s 786 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU s 788 " --> pdb=" O LEU s 701 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU s 701 " --> pdb=" O LEU s 788 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 's' and resid 31 through 32 Processing sheet with id=AA4, first strand: chain 's' and resid 42 through 43 Processing sheet with id=AA5, first strand: chain 's' and resid 65 through 66 removed outlier: 4.179A pdb=" N VAL s 88 " --> pdb=" O LYS s 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 's' and resid 69 through 70 Processing sheet with id=AA7, first strand: chain 's' and resid 116 through 120 removed outlier: 4.317A pdb=" N THR s 125 " --> pdb=" O LEU s 312 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 's' and resid 221 through 222 removed outlier: 3.585A pdb=" N VAL s 222 " --> pdb=" O GLY s 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 's' and resid 164 through 167 removed outlier: 6.695A pdb=" N LEU s 165 " --> pdb=" O LYS s 176 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS s 176 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 's' and resid 250 through 251 Processing sheet with id=AB2, first strand: chain 's' and resid 359 through 362 removed outlier: 3.543A pdb=" N VAL s 393 " --> pdb=" O ILE s 366 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 's' and resid 406 through 409 removed outlier: 3.686A pdb=" N GLU s 412 " --> pdb=" O PHE s 409 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 's' and resid 458 through 459 Processing sheet with id=AB5, first strand: chain 's' and resid 511 through 512 removed outlier: 3.622A pdb=" N SER s 541 " --> pdb=" O MET s 525 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 's' and resid 530 through 531 Processing sheet with id=AB7, first strand: chain 's' and resid 551 through 557 removed outlier: 4.733A pdb=" N ALA s 553 " --> pdb=" O ILE s 564 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE s 564 " --> pdb=" O ALA s 553 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 's' and resid 598 through 600 Processing sheet with id=AB9, first strand: chain 's' and resid 607 through 608 removed outlier: 3.732A pdb=" N ASN s 608 " --> pdb=" O THR s 613 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR s 613 " --> pdb=" O ASN s 608 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 's' and resid 685 through 686 Processing sheet with id=AC2, first strand: chain 't' and resid 4 through 8 removed outlier: 3.842A pdb=" N GLY t 780 " --> pdb=" O ASN t 709 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU t 784 " --> pdb=" O ARG t 705 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG t 705 " --> pdb=" O GLU t 784 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN t 786 " --> pdb=" O LEU t 703 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU t 703 " --> pdb=" O ASN t 786 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU t 788 " --> pdb=" O LEU t 701 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU t 701 " --> pdb=" O LEU t 788 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 't' and resid 4 through 8 removed outlier: 3.842A pdb=" N GLY t 780 " --> pdb=" O ASN t 709 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU t 784 " --> pdb=" O ARG t 705 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG t 705 " --> pdb=" O GLU t 784 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN t 786 " --> pdb=" O LEU t 703 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU t 703 " --> pdb=" O ASN t 786 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU t 788 " --> pdb=" O LEU t 701 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU t 701 " --> pdb=" O LEU t 788 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 't' and resid 31 through 32 Processing sheet with id=AC5, first strand: chain 't' and resid 42 through 43 Processing sheet with id=AC6, first strand: chain 't' and resid 48 through 49 removed outlier: 4.944A pdb=" N ILE t 564 " --> pdb=" O ALA t 553 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA t 553 " --> pdb=" O ILE t 564 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 't' and resid 65 through 66 removed outlier: 4.180A pdb=" N VAL t 88 " --> pdb=" O LYS t 96 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 't' and resid 69 through 70 Processing sheet with id=AC9, first strand: chain 't' and resid 116 through 120 removed outlier: 4.317A pdb=" N THR t 125 " --> pdb=" O LEU t 312 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 't' and resid 221 through 222 removed outlier: 3.586A pdb=" N VAL t 222 " --> pdb=" O GLY t 152 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 't' and resid 164 through 167 removed outlier: 6.694A pdb=" N LEU t 165 " --> pdb=" O LYS t 176 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS t 176 " --> pdb=" O LEU t 165 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 't' and resid 250 through 251 Processing sheet with id=AD4, first strand: chain 't' and resid 359 through 362 removed outlier: 3.545A pdb=" N VAL t 393 " --> pdb=" O ILE t 366 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 't' and resid 406 through 409 removed outlier: 3.687A pdb=" N GLU t 412 " --> pdb=" O PHE t 409 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 't' and resid 458 through 459 Processing sheet with id=AD7, first strand: chain 't' and resid 511 through 512 removed outlier: 3.620A pdb=" N SER t 541 " --> pdb=" O MET t 525 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 't' and resid 530 through 531 Processing sheet with id=AD9, first strand: chain 't' and resid 598 through 600 Processing sheet with id=AE1, first strand: chain 't' and resid 607 through 608 removed outlier: 3.732A pdb=" N ASN t 608 " --> pdb=" O THR t 613 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR t 613 " --> pdb=" O ASN t 608 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 't' and resid 685 through 686 Processing sheet with id=AE3, first strand: chain 'u' and resid 4 through 8 removed outlier: 3.842A pdb=" N GLY u 780 " --> pdb=" O ASN u 709 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU u 784 " --> pdb=" O ARG u 705 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG u 705 " --> pdb=" O GLU u 784 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASN u 786 " --> pdb=" O LEU u 703 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU u 703 " --> pdb=" O ASN u 786 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU u 788 " --> pdb=" O LEU u 701 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU u 701 " --> pdb=" O LEU u 788 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'u' and resid 4 through 8 removed outlier: 3.842A pdb=" N GLY u 780 " --> pdb=" O ASN u 709 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU u 784 " --> pdb=" O ARG u 705 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG u 705 " --> pdb=" O GLU u 784 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASN u 786 " --> pdb=" O LEU u 703 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU u 703 " --> pdb=" O ASN u 786 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU u 788 " --> pdb=" O LEU u 701 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU u 701 " --> pdb=" O LEU u 788 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'u' and resid 31 through 32 Processing sheet with id=AE6, first strand: chain 'u' and resid 42 through 43 Processing sheet with id=AE7, first strand: chain 'u' and resid 65 through 66 removed outlier: 4.179A pdb=" N VAL u 88 " --> pdb=" O LYS u 96 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'u' and resid 69 through 70 Processing sheet with id=AE9, first strand: chain 'u' and resid 116 through 120 removed outlier: 4.317A pdb=" N THR u 125 " --> pdb=" O LEU u 312 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'u' and resid 221 through 222 removed outlier: 3.585A pdb=" N VAL u 222 " --> pdb=" O GLY u 152 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'u' and resid 164 through 167 removed outlier: 6.693A pdb=" N LEU u 165 " --> pdb=" O LYS u 176 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS u 176 " --> pdb=" O LEU u 165 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'u' and resid 250 through 251 Processing sheet with id=AF4, first strand: chain 'u' and resid 359 through 362 removed outlier: 3.544A pdb=" N VAL u 393 " --> pdb=" O ILE u 366 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'u' and resid 406 through 409 removed outlier: 3.687A pdb=" N GLU u 412 " --> pdb=" O PHE u 409 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'u' and resid 458 through 459 Processing sheet with id=AF7, first strand: chain 'u' and resid 511 through 512 removed outlier: 3.621A pdb=" N SER u 541 " --> pdb=" O MET u 525 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'u' and resid 530 through 531 Processing sheet with id=AF9, first strand: chain 'u' and resid 551 through 557 removed outlier: 4.734A pdb=" N ALA u 553 " --> pdb=" O ILE u 564 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE u 564 " --> pdb=" O ALA u 553 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'u' and resid 598 through 600 Processing sheet with id=AG2, first strand: chain 'u' and resid 607 through 608 removed outlier: 3.730A pdb=" N ASN u 608 " --> pdb=" O THR u 613 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR u 613 " --> pdb=" O ASN u 608 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'u' and resid 685 through 686 Processing sheet with id=AG4, first strand: chain 'v' and resid 4 through 8 removed outlier: 3.840A pdb=" N GLY v 780 " --> pdb=" O ASN v 709 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU v 784 " --> pdb=" O ARG v 705 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG v 705 " --> pdb=" O GLU v 784 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN v 786 " --> pdb=" O LEU v 703 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU v 703 " --> pdb=" O ASN v 786 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU v 788 " --> pdb=" O LEU v 701 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU v 701 " --> pdb=" O LEU v 788 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'v' and resid 4 through 8 removed outlier: 3.840A pdb=" N GLY v 780 " --> pdb=" O ASN v 709 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU v 784 " --> pdb=" O ARG v 705 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG v 705 " --> pdb=" O GLU v 784 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN v 786 " --> pdb=" O LEU v 703 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU v 703 " --> pdb=" O ASN v 786 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU v 788 " --> pdb=" O LEU v 701 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU v 701 " --> pdb=" O LEU v 788 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'v' and resid 31 through 32 Processing sheet with id=AG7, first strand: chain 'v' and resid 42 through 43 Processing sheet with id=AG8, first strand: chain 'v' and resid 48 through 49 removed outlier: 4.944A pdb=" N ILE v 564 " --> pdb=" O ALA v 553 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA v 553 " --> pdb=" O ILE v 564 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'v' and resid 65 through 66 removed outlier: 4.179A pdb=" N VAL v 88 " --> pdb=" O LYS v 96 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'v' and resid 69 through 70 Processing sheet with id=AH2, first strand: chain 'v' and resid 116 through 120 removed outlier: 4.317A pdb=" N THR v 125 " --> pdb=" O LEU v 312 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'v' and resid 221 through 222 removed outlier: 3.586A pdb=" N VAL v 222 " --> pdb=" O GLY v 152 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'v' and resid 164 through 167 removed outlier: 6.693A pdb=" N LEU v 165 " --> pdb=" O LYS v 176 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS v 176 " --> pdb=" O LEU v 165 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'v' and resid 250 through 251 Processing sheet with id=AH6, first strand: chain 'v' and resid 359 through 362 removed outlier: 3.544A pdb=" N VAL v 393 " --> pdb=" O ILE v 366 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'v' and resid 406 through 409 removed outlier: 3.687A pdb=" N GLU v 412 " --> pdb=" O PHE v 409 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'v' and resid 458 through 459 Processing sheet with id=AH9, first strand: chain 'v' and resid 511 through 512 removed outlier: 3.623A pdb=" N SER v 541 " --> pdb=" O MET v 525 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'v' and resid 530 through 531 Processing sheet with id=AI2, first strand: chain 'v' and resid 598 through 600 Processing sheet with id=AI3, first strand: chain 'v' and resid 607 through 608 removed outlier: 3.730A pdb=" N ASN v 608 " --> pdb=" O THR v 613 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR v 613 " --> pdb=" O ASN v 608 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'v' and resid 685 through 686 Processing sheet with id=AI5, first strand: chain 'w' and resid 4 through 8 removed outlier: 3.841A pdb=" N GLY w 780 " --> pdb=" O ASN w 709 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU w 784 " --> pdb=" O ARG w 705 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG w 705 " --> pdb=" O GLU w 784 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASN w 786 " --> pdb=" O LEU w 703 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU w 703 " --> pdb=" O ASN w 786 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU w 788 " --> pdb=" O LEU w 701 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU w 701 " --> pdb=" O LEU w 788 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'w' and resid 4 through 8 removed outlier: 3.841A pdb=" N GLY w 780 " --> pdb=" O ASN w 709 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU w 784 " --> pdb=" O ARG w 705 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG w 705 " --> pdb=" O GLU w 784 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASN w 786 " --> pdb=" O LEU w 703 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU w 703 " --> pdb=" O ASN w 786 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU w 788 " --> pdb=" O LEU w 701 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU w 701 " --> pdb=" O LEU w 788 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'w' and resid 31 through 32 Processing sheet with id=AI8, first strand: chain 'w' and resid 42 through 43 Processing sheet with id=AI9, first strand: chain 'w' and resid 48 through 49 removed outlier: 4.944A pdb=" N ILE w 564 " --> pdb=" O ALA w 553 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA w 553 " --> pdb=" O ILE w 564 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'w' and resid 65 through 66 removed outlier: 4.179A pdb=" N VAL w 88 " --> pdb=" O LYS w 96 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'w' and resid 69 through 70 Processing sheet with id=AJ3, first strand: chain 'w' and resid 116 through 120 removed outlier: 4.318A pdb=" N THR w 125 " --> pdb=" O LEU w 312 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'w' and resid 221 through 222 removed outlier: 3.586A pdb=" N VAL w 222 " --> pdb=" O GLY w 152 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'w' and resid 164 through 167 removed outlier: 6.694A pdb=" N LEU w 165 " --> pdb=" O LYS w 176 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS w 176 " --> pdb=" O LEU w 165 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'w' and resid 250 through 251 Processing sheet with id=AJ7, first strand: chain 'w' and resid 359 through 362 removed outlier: 3.543A pdb=" N VAL w 393 " --> pdb=" O ILE w 366 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'w' and resid 406 through 409 removed outlier: 3.687A pdb=" N GLU w 412 " --> pdb=" O PHE w 409 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'w' and resid 458 through 459 Processing sheet with id=AK1, first strand: chain 'w' and resid 511 through 512 removed outlier: 3.621A pdb=" N SER w 541 " --> pdb=" O MET w 525 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'w' and resid 530 through 531 Processing sheet with id=AK3, first strand: chain 'w' and resid 598 through 600 Processing sheet with id=AK4, first strand: chain 'w' and resid 607 through 608 removed outlier: 3.731A pdb=" N ASN w 608 " --> pdb=" O THR w 613 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR w 613 " --> pdb=" O ASN w 608 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'w' and resid 685 through 686 Processing sheet with id=AK6, first strand: chain 'x' and resid 4 through 8 removed outlier: 3.839A pdb=" N GLY x 780 " --> pdb=" O ASN x 709 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU x 784 " --> pdb=" O ARG x 705 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ARG x 705 " --> pdb=" O GLU x 784 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASN x 786 " --> pdb=" O LEU x 703 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU x 703 " --> pdb=" O ASN x 786 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU x 788 " --> pdb=" O LEU x 701 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU x 701 " --> pdb=" O LEU x 788 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'x' and resid 4 through 8 removed outlier: 3.839A pdb=" N GLY x 780 " --> pdb=" O ASN x 709 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU x 784 " --> pdb=" O ARG x 705 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ARG x 705 " --> pdb=" O GLU x 784 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASN x 786 " --> pdb=" O LEU x 703 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU x 703 " --> pdb=" O ASN x 786 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU x 788 " --> pdb=" O LEU x 701 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU x 701 " --> pdb=" O LEU x 788 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'x' and resid 31 through 32 Processing sheet with id=AK9, first strand: chain 'x' and resid 42 through 43 Processing sheet with id=AL1, first strand: chain 'x' and resid 48 through 49 removed outlier: 3.574A pdb=" N ARG x 575 " --> pdb=" O VAL x 49 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE x 564 " --> pdb=" O ALA x 553 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA x 553 " --> pdb=" O ILE x 564 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'x' and resid 65 through 66 removed outlier: 4.179A pdb=" N VAL x 88 " --> pdb=" O LYS x 96 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'x' and resid 69 through 70 Processing sheet with id=AL4, first strand: chain 'x' and resid 116 through 120 removed outlier: 4.317A pdb=" N THR x 125 " --> pdb=" O LEU x 312 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'x' and resid 221 through 222 removed outlier: 3.586A pdb=" N VAL x 222 " --> pdb=" O GLY x 152 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'x' and resid 164 through 167 removed outlier: 6.695A pdb=" N LEU x 165 " --> pdb=" O LYS x 176 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS x 176 " --> pdb=" O LEU x 165 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'x' and resid 250 through 251 Processing sheet with id=AL8, first strand: chain 'x' and resid 359 through 362 removed outlier: 3.544A pdb=" N VAL x 393 " --> pdb=" O ILE x 366 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'x' and resid 406 through 409 removed outlier: 3.686A pdb=" N GLU x 412 " --> pdb=" O PHE x 409 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'x' and resid 458 through 459 Processing sheet with id=AM2, first strand: chain 'x' and resid 511 through 512 removed outlier: 3.622A pdb=" N SER x 541 " --> pdb=" O MET x 525 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'x' and resid 530 through 531 Processing sheet with id=AM4, first strand: chain 'x' and resid 598 through 600 Processing sheet with id=AM5, first strand: chain 'x' and resid 607 through 608 removed outlier: 3.733A pdb=" N ASN x 608 " --> pdb=" O THR x 613 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR x 613 " --> pdb=" O ASN x 608 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'x' and resid 685 through 686 715 hydrogen bonds defined for protein. 1605 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: 9.89 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7814 1.33 - 1.45: 9897 1.45 - 1.57: 20887 1.57 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 38748 Sorted by residual: bond pdb=" N PRO u 64 " pdb=" CD PRO u 64 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.20e+01 bond pdb=" N PRO w 64 " pdb=" CD PRO w 64 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" N PRO v 64 " pdb=" CD PRO v 64 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" N PRO s 64 " pdb=" CD PRO s 64 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.95e+01 bond pdb=" N PRO t 64 " pdb=" CD PRO t 64 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.94e+01 ... (remaining 38743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.58: 51873 4.58 - 9.17: 649 9.17 - 13.75: 133 13.75 - 18.33: 25 18.33 - 22.92: 12 Bond angle restraints: 52692 Sorted by residual: angle pdb=" N GLY s 218 " pdb=" CA GLY s 218 " pdb=" C GLY s 218 " ideal model delta sigma weight residual 113.18 133.49 -20.31 2.37e+00 1.78e-01 7.34e+01 angle pdb=" N GLY u 218 " pdb=" CA GLY u 218 " pdb=" C GLY u 218 " ideal model delta sigma weight residual 113.18 133.43 -20.25 2.37e+00 1.78e-01 7.30e+01 angle pdb=" N GLY v 218 " pdb=" CA GLY v 218 " pdb=" C GLY v 218 " ideal model delta sigma weight residual 113.18 133.42 -20.24 2.37e+00 1.78e-01 7.29e+01 angle pdb=" N GLY t 218 " pdb=" CA GLY t 218 " pdb=" C GLY t 218 " ideal model delta sigma weight residual 113.18 133.40 -20.22 2.37e+00 1.78e-01 7.28e+01 angle pdb=" N GLY x 218 " pdb=" CA GLY x 218 " pdb=" C GLY x 218 " ideal model delta sigma weight residual 113.18 133.40 -20.22 2.37e+00 1.78e-01 7.28e+01 ... (remaining 52687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.69: 21800 23.69 - 47.39: 864 47.39 - 71.08: 62 71.08 - 94.78: 8 94.78 - 118.47: 12 Dihedral angle restraints: 22746 sinusoidal: 9030 harmonic: 13716 Sorted by residual: dihedral pdb=" CA ALA u 688 " pdb=" C ALA u 688 " pdb=" N ASP u 689 " pdb=" CA ASP u 689 " ideal model delta harmonic sigma weight residual 180.00 61.53 118.47 0 5.00e+00 4.00e-02 5.61e+02 dihedral pdb=" CA ALA w 688 " pdb=" C ALA w 688 " pdb=" N ASP w 689 " pdb=" CA ASP w 689 " ideal model delta harmonic sigma weight residual 180.00 61.53 118.47 0 5.00e+00 4.00e-02 5.61e+02 dihedral pdb=" CA ALA t 688 " pdb=" C ALA t 688 " pdb=" N ASP t 689 " pdb=" CA ASP t 689 " ideal model delta harmonic sigma weight residual 180.00 61.54 118.46 0 5.00e+00 4.00e-02 5.61e+02 ... (remaining 22743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 5038 0.111 - 0.223: 518 0.223 - 0.334: 78 0.334 - 0.446: 1 0.446 - 0.557: 5 Chirality restraints: 5640 Sorted by residual: chirality pdb=" CA PHE u 50 " pdb=" N PHE u 50 " pdb=" C PHE u 50 " pdb=" CB PHE u 50 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.75e+00 chirality pdb=" CA PHE t 50 " pdb=" N PHE t 50 " pdb=" C PHE t 50 " pdb=" CB PHE t 50 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA PHE s 50 " pdb=" N PHE s 50 " pdb=" C PHE s 50 " pdb=" CB PHE s 50 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.24e+00 ... (remaining 5637 not shown) Planarity restraints: 6918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP x 595 " -0.021 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C ASP x 595 " 0.075 2.00e-02 2.50e+03 pdb=" O ASP x 595 " -0.029 2.00e-02 2.50e+03 pdb=" N MET x 596 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP v 595 " -0.021 2.00e-02 2.50e+03 4.35e-02 1.90e+01 pdb=" C ASP v 595 " 0.075 2.00e-02 2.50e+03 pdb=" O ASP v 595 " -0.029 2.00e-02 2.50e+03 pdb=" N MET v 596 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP u 595 " 0.021 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C ASP u 595 " -0.075 2.00e-02 2.50e+03 pdb=" O ASP u 595 " 0.029 2.00e-02 2.50e+03 pdb=" N MET u 596 " 0.025 2.00e-02 2.50e+03 ... (remaining 6915 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 70 2.35 - 2.99: 19403 2.99 - 3.63: 55470 3.63 - 4.26: 86754 4.26 - 4.90: 144020 Nonbonded interactions: 305717 Sorted by model distance: nonbonded pdb=" O GLY u 55 " pdb=" OD1 ASN u 570 " model vdw 1.717 3.040 nonbonded pdb=" O GLY x 55 " pdb=" OD1 ASN x 570 " model vdw 1.735 3.040 nonbonded pdb=" O GLY s 55 " pdb=" OD1 ASN s 570 " model vdw 1.916 3.040 nonbonded pdb=" O GLY v 55 " pdb=" OD1 ASN v 570 " model vdw 1.947 3.040 nonbonded pdb=" O GLY w 55 " pdb=" OD1 ASN w 570 " model vdw 1.962 3.040 ... (remaining 305712 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: 0.06 Found NCS groups: ncs_group { reference = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } 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=0.10 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 35.270 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.008 0.074 38748 Z= 0.412 Angle : 1.495 22.916 52692 Z= 0.816 Chirality : 0.073 0.557 5640 Planarity : 0.007 0.068 6918 Dihedral : 12.884 118.469 13986 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 1.15 % Allowed : 16.26 % Favored : 82.59 % Rotamer: Outliers : 1.21 % Allowed : 7.25 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.33 % Twisted Proline : 6.02 % Twisted General : 3.72 % 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: -5.15 (0.10), residues: 4716 helix: -5.02 (0.10), residues: 156 sheet: -3.32 (0.12), residues: 1584 loop : -3.55 (0.09), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG v 87 TYR 0.030 0.004 TYR u 767 PHE 0.052 0.004 PHE x 50 TRP 0.047 0.004 TRP v 297 HIS 0.011 0.003 HIS u 491 Details of bonding type rmsd covalent geometry : bond 0.00836 (38748) covalent geometry : angle 1.49486 (52692) hydrogen bonds : bond 0.27007 ( 661) hydrogen bonds : angle 11.34656 ( 1605) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 1137 time to evaluate : 1.368 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: 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: s 29 SER cc_start: 0.8989 (m) cc_final: 0.8596 (t) REVERT: s 239 TYR cc_start: 0.8465 (t80) cc_final: 0.7999 (t80) REVERT: s 278 ASP cc_start: 0.8249 (m-30) cc_final: 0.8029 (t0) REVERT: s 342 SER cc_start: 0.8131 (m) cc_final: 0.7920 (p) REVERT: s 367 ILE cc_start: 0.9070 (mp) cc_final: 0.8799 (mm) REVERT: s 374 TYR cc_start: 0.8245 (m-10) cc_final: 0.7894 (m-80) REVERT: s 417 SER cc_start: 0.9144 (m) cc_final: 0.8821 (p) REVERT: s 567 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7836 (m-40) REVERT: s 631 ILE cc_start: 0.9514 (mt) cc_final: 0.9127 (tt) REVERT: s 741 LEU cc_start: 0.9213 (tp) cc_final: 0.8884 (tt) REVERT: t 228 GLN cc_start: 0.8659 (mp-120) cc_final: 0.8014 (mp10) REVERT: t 367 ILE cc_start: 0.8913 (mp) cc_final: 0.8640 (mm) REVERT: t 788 LEU cc_start: 0.8901 (tm) cc_final: 0.8633 (tp) REVERT: u 336 ASP cc_start: 0.7688 (p0) cc_final: 0.7342 (p0) REVERT: u 352 PHE cc_start: 0.8830 (m-10) cc_final: 0.8267 (m-80) REVERT: u 367 ILE cc_start: 0.8943 (mp) cc_final: 0.8731 (mm) REVERT: u 417 SER cc_start: 0.9028 (m) cc_final: 0.8752 (p) REVERT: u 439 LEU cc_start: 0.9195 (tm) cc_final: 0.8977 (tp) REVERT: u 477 GLN cc_start: 0.8560 (mt0) cc_final: 0.7964 (mt0) REVERT: u 542 HIS cc_start: 0.7343 (m-70) cc_final: 0.6980 (m-70) REVERT: u 550 GLN cc_start: 0.8278 (mt0) cc_final: 0.7726 (mp10) REVERT: v 20 ASP cc_start: 0.7976 (p0) cc_final: 0.7651 (t0) REVERT: v 180 PRO cc_start: 0.8737 (Cg_endo) cc_final: 0.8425 (Cg_exo) REVERT: v 255 SER cc_start: 0.9029 (m) cc_final: 0.8823 (p) REVERT: v 269 ILE cc_start: 0.9223 (mm) cc_final: 0.8988 (tp) REVERT: v 342 SER cc_start: 0.8291 (m) cc_final: 0.7975 (p) REVERT: v 417 SER cc_start: 0.8985 (m) cc_final: 0.8673 (t) REVERT: v 644 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6270 (tm-30) REVERT: v 701 LEU cc_start: 0.9398 (tm) cc_final: 0.9185 (tp) REVERT: v 742 ARG cc_start: 0.8140 (mmt180) cc_final: 0.7835 (mmm160) REVERT: w 336 ASP cc_start: 0.7875 (p0) cc_final: 0.7644 (p0) REVERT: w 367 ILE cc_start: 0.8867 (mp) cc_final: 0.8517 (mm) REVERT: w 425 THR cc_start: 0.8610 (p) cc_final: 0.8394 (p) REVERT: w 550 GLN cc_start: 0.8116 (mt0) cc_final: 0.7885 (mp10) REVERT: x 138 THR cc_start: 0.9144 (p) cc_final: 0.8851 (p) REVERT: x 336 ASP cc_start: 0.8080 (p0) cc_final: 0.7864 (p0) REVERT: x 352 PHE cc_start: 0.8694 (m-10) cc_final: 0.8460 (m-80) REVERT: x 417 SER cc_start: 0.9156 (m) cc_final: 0.8895 (p) REVERT: x 441 THR cc_start: 0.8945 (p) cc_final: 0.8673 (p) REVERT: x 477 GLN cc_start: 0.8118 (mt0) cc_final: 0.7342 (mt0) REVERT: x 788 LEU cc_start: 0.8824 (tm) cc_final: 0.8579 (tp) outliers start: 50 outliers final: 13 residues processed: 1175 average time/residue: 0.2499 time to fit residues: 459.1348 Evaluate side-chains 568 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 554 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 64 PRO Chi-restraints excluded: chain s residue 414 LEU Chi-restraints excluded: chain s residue 567 ASN Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain u residue 64 PRO Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 60 LEU Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 60 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 0.7980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 31 GLN s 67 HIS s 114 ASN ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 252 GLN s 310 HIS s 376 ASN ** s 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 457 ASN s 494 ASN s 532 ASN ** s 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 570 ASN s 672 ASN s 777 ASN t 6 GLN t 62 GLN t 74 HIS t 111 ASN t 114 ASN ** t 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 189 ASN t 245 ASN t 252 GLN t 376 ASN t 457 ASN t 494 ASN ** t 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 764 ASN t 777 ASN u 67 HIS u 114 ASN u 187 HIS u 207 ASN ** u 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 376 ASN u 457 ASN u 494 ASN u 567 ASN u 570 ASN u 672 ASN u 764 ASN u 777 ASN v 10 ASN v 67 HIS v 74 HIS v 114 ASN ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 189 ASN v 207 ASN v 252 GLN v 376 ASN v 457 ASN v 532 ASN ** v 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 764 ASN v 777 ASN w 6 GLN w 114 ASN w 168 HIS ** w 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 207 ASN w 245 ASN w 252 GLN w 260 ASN w 376 ASN w 457 ASN w 494 ASN w 747 ASN w 764 ASN w 777 ASN x 10 ASN x 31 GLN x 67 HIS x 74 HIS x 114 ASN x 187 HIS ** x 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 310 HIS x 376 ASN x 457 ASN x 494 ASN x 570 ASN x 672 ASN x 726 ASN x 764 ASN ** x 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.118670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.091763 restraints weight = 75861.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.093978 restraints weight = 40088.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095410 restraints weight = 26233.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.096297 restraints weight = 19694.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.096785 restraints weight = 16411.688| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38748 Z= 0.192 Angle : 1.043 18.929 52692 Z= 0.529 Chirality : 0.056 0.271 5640 Planarity : 0.006 0.068 6918 Dihedral : 10.491 78.397 5233 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.76 % Allowed : 17.01 % Favored : 82.23 % Rotamer: Outliers : 3.40 % Allowed : 14.90 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.33 % Twisted Proline : 2.78 % Twisted General : 1.95 % 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: -4.64 (0.11), residues: 4716 helix: -4.19 (0.23), residues: 132 sheet: -2.88 (0.12), residues: 1650 loop : -3.28 (0.10), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG u 283 TYR 0.020 0.002 TYR w 405 PHE 0.028 0.002 PHE s 352 TRP 0.033 0.002 TRP t 305 HIS 0.011 0.002 HIS t 74 Details of bonding type rmsd covalent geometry : bond 0.00422 (38748) covalent geometry : angle 1.04259 (52692) hydrogen bonds : bond 0.04906 ( 661) hydrogen bonds : angle 8.33249 ( 1605) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 619 time to evaluate : 1.516 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: s 29 SER cc_start: 0.8989 (m) cc_final: 0.8390 (t) REVERT: s 278 ASP cc_start: 0.8156 (m-30) cc_final: 0.7823 (t0) REVERT: s 308 MET cc_start: 0.8740 (mmm) cc_final: 0.8075 (mmm) REVERT: s 364 GLU cc_start: 0.6750 (mp0) cc_final: 0.6351 (pm20) REVERT: s 367 ILE cc_start: 0.9125 (mp) cc_final: 0.8900 (mm) REVERT: s 460 PHE cc_start: 0.8729 (m-10) cc_final: 0.8434 (m-10) REVERT: s 550 GLN cc_start: 0.7986 (mt0) cc_final: 0.7725 (mp10) REVERT: s 631 ILE cc_start: 0.9573 (mt) cc_final: 0.9249 (tt) REVERT: t 29 SER cc_start: 0.9269 (m) cc_final: 0.8720 (t) REVERT: t 228 GLN cc_start: 0.8387 (mp-120) cc_final: 0.8079 (mp10) REVERT: t 255 SER cc_start: 0.9126 (m) cc_final: 0.8904 (p) REVERT: t 272 ASP cc_start: 0.8941 (t0) cc_final: 0.8270 (t0) REVERT: t 314 ARG cc_start: 0.7909 (ttt90) cc_final: 0.7393 (tpt-90) REVERT: t 326 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7392 (mm-30) REVERT: t 336 ASP cc_start: 0.7515 (p0) cc_final: 0.7284 (p0) REVERT: t 367 ILE cc_start: 0.9040 (mp) cc_final: 0.8693 (mm) REVERT: t 416 TRP cc_start: 0.8840 (m-10) cc_final: 0.8540 (m-10) REVERT: t 718 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7605 (mm) REVERT: t 721 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6653 (tm-30) REVERT: u 29 SER cc_start: 0.9111 (m) cc_final: 0.8766 (t) REVERT: u 71 ARG cc_start: 0.7291 (ttm110) cc_final: 0.6861 (mtt-85) REVERT: u 324 TRP cc_start: 0.8409 (p-90) cc_final: 0.7997 (p-90) REVERT: u 336 ASP cc_start: 0.7540 (p0) cc_final: 0.7301 (p0) REVERT: u 342 SER cc_start: 0.7927 (m) cc_final: 0.7674 (p) REVERT: u 367 ILE cc_start: 0.9079 (mp) cc_final: 0.8850 (mm) REVERT: u 405 TYR cc_start: 0.7527 (m-80) cc_final: 0.7045 (m-80) REVERT: u 416 TRP cc_start: 0.9168 (m-10) cc_final: 0.8328 (m-10) REVERT: u 417 SER cc_start: 0.8989 (m) cc_final: 0.8655 (t) REVERT: u 477 GLN cc_start: 0.8469 (mt0) cc_final: 0.8149 (mt0) REVERT: u 550 GLN cc_start: 0.8258 (mt0) cc_final: 0.7838 (mp10) REVERT: u 561 MET cc_start: 0.8457 (tpp) cc_final: 0.8003 (ttt) REVERT: v 255 SER cc_start: 0.9119 (m) cc_final: 0.8834 (p) REVERT: v 308 MET cc_start: 0.8527 (mmm) cc_final: 0.7951 (mmm) REVERT: v 314 ARG cc_start: 0.7686 (ttt90) cc_final: 0.7456 (ttt90) REVERT: v 352 PHE cc_start: 0.8249 (m-10) cc_final: 0.8042 (m-10) REVERT: v 364 GLU cc_start: 0.7164 (mp0) cc_final: 0.6950 (mp0) REVERT: v 405 TYR cc_start: 0.7550 (m-80) cc_final: 0.7290 (m-80) REVERT: v 417 SER cc_start: 0.8928 (m) cc_final: 0.8393 (t) REVERT: v 644 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6480 (tm-30) REVERT: v 701 LEU cc_start: 0.9430 (tm) cc_final: 0.9148 (tp) REVERT: v 742 ARG cc_start: 0.8222 (mmt180) cc_final: 0.7778 (mmp-170) REVERT: v 788 LEU cc_start: 0.8285 (tt) cc_final: 0.8047 (tp) REVERT: w 220 ILE cc_start: 0.8751 (mm) cc_final: 0.8477 (mm) REVERT: w 239 TYR cc_start: 0.8485 (t80) cc_final: 0.8180 (t80) REVERT: w 255 SER cc_start: 0.9205 (m) cc_final: 0.8690 (p) REVERT: w 272 ASP cc_start: 0.8889 (t0) cc_final: 0.8455 (t0) REVERT: w 283 ARG cc_start: 0.8596 (ttt90) cc_final: 0.8370 (ttt90) REVERT: w 308 MET cc_start: 0.8410 (mmm) cc_final: 0.7759 (mmm) REVERT: w 314 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7417 (ttm-80) REVERT: w 367 ILE cc_start: 0.9019 (mp) cc_final: 0.8640 (mm) REVERT: w 416 TRP cc_start: 0.8961 (m-10) cc_final: 0.8743 (m-10) REVERT: w 566 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8039 (mtm-85) REVERT: w 697 ASP cc_start: 0.7197 (p0) cc_final: 0.6993 (p0) REVERT: w 718 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7299 (mt) REVERT: x 138 THR cc_start: 0.9006 (p) cc_final: 0.8789 (p) REVERT: x 272 ASP cc_start: 0.9209 (t70) cc_final: 0.8662 (t0) REVERT: x 308 MET cc_start: 0.8741 (mmm) cc_final: 0.8339 (mmm) REVERT: x 352 PHE cc_start: 0.8281 (m-10) cc_final: 0.7801 (m-80) REVERT: x 364 GLU cc_start: 0.6925 (mp0) cc_final: 0.6708 (mp0) REVERT: x 405 TYR cc_start: 0.7691 (m-80) cc_final: 0.7271 (m-80) REVERT: x 417 SER cc_start: 0.9038 (m) cc_final: 0.8698 (t) REVERT: x 550 GLN cc_start: 0.8345 (mt0) cc_final: 0.7844 (mp10) REVERT: x 561 MET cc_start: 0.8219 (tpp) cc_final: 0.7812 (ttt) REVERT: x 718 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7791 (mt) outliers start: 140 outliers final: 50 residues processed: 737 average time/residue: 0.2294 time to fit residues: 273.6560 Evaluate side-chains 528 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 474 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 136 LYS Chi-restraints excluded: chain s residue 138 THR Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 290 VAL Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 414 LEU Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain s residue 770 SER Chi-restraints excluded: chain t residue 26 ASP Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 531 LEU Chi-restraints excluded: chain t residue 572 PHE Chi-restraints excluded: chain t residue 718 ILE Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 344 VAL Chi-restraints excluded: chain u residue 346 SER Chi-restraints excluded: chain u residue 393 VAL Chi-restraints excluded: chain u residue 395 VAL Chi-restraints excluded: chain u residue 407 VAL Chi-restraints excluded: chain u residue 770 SER Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 74 HIS Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 572 PHE Chi-restraints excluded: chain v residue 647 THR Chi-restraints excluded: chain v residue 687 THR Chi-restraints excluded: chain v residue 725 SER Chi-restraints excluded: chain v residue 764 ASN Chi-restraints excluded: chain v residue 770 SER Chi-restraints excluded: chain v residue 781 CYS Chi-restraints excluded: chain v residue 792 SER Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 92 SER Chi-restraints excluded: chain w residue 314 ARG Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 572 PHE Chi-restraints excluded: chain w residue 585 LEU Chi-restraints excluded: chain w residue 718 ILE Chi-restraints excluded: chain w residue 781 CYS Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 290 VAL Chi-restraints excluded: chain x residue 304 LEU Chi-restraints excluded: chain x residue 572 PHE Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 718 ILE Chi-restraints excluded: chain x residue 770 SER Chi-restraints excluded: chain x residue 781 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 346 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 380 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 213 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 454 optimal weight: 0.7980 chunk 368 optimal weight: 0.4980 chunk 344 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 395 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 150 GLN ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 542 HIS s 747 ASN ** t 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 67 HIS v 6 GLN v 10 ASN v 150 GLN ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 661 ASN w 10 ASN ** w 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 190 ASN w 672 ASN x 145 ASN x 207 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.119464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.090991 restraints weight = 75159.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.093336 restraints weight = 39424.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.094815 restraints weight = 25767.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.095754 restraints weight = 19497.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.096327 restraints weight = 16282.789| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 38748 Z= 0.173 Angle : 0.966 19.168 52692 Z= 0.488 Chirality : 0.054 0.243 5640 Planarity : 0.005 0.069 6918 Dihedral : 9.333 57.644 5218 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.76 % Allowed : 16.71 % Favored : 82.53 % Rotamer: Outliers : 3.76 % Allowed : 16.42 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.33 % Twisted Proline : 2.78 % Twisted General : 1.60 % 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: -4.46 (0.11), residues: 4716 helix: -3.82 (0.23), residues: 162 sheet: -2.86 (0.12), residues: 1548 loop : -3.11 (0.10), residues: 3006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG v 628 TYR 0.022 0.002 TYR v 473 PHE 0.032 0.002 PHE u 352 TRP 0.030 0.002 TRP v 416 HIS 0.016 0.002 HIS v 74 Details of bonding type rmsd covalent geometry : bond 0.00385 (38748) covalent geometry : angle 0.96564 (52692) hydrogen bonds : bond 0.03879 ( 661) hydrogen bonds : angle 7.60045 ( 1605) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 552 time to evaluate : 1.494 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: s 29 SER cc_start: 0.9059 (m) cc_final: 0.8347 (t) REVERT: s 78 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.6917 (t80) REVERT: s 266 MET cc_start: 0.8367 (mtt) cc_final: 0.8032 (ttm) REVERT: s 308 MET cc_start: 0.8804 (mmm) cc_final: 0.8262 (mtm) REVERT: s 364 GLU cc_start: 0.6748 (mp0) cc_final: 0.6307 (pm20) REVERT: s 367 ILE cc_start: 0.9172 (mp) cc_final: 0.8909 (mm) REVERT: s 403 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7983 (tt) REVERT: s 550 GLN cc_start: 0.8052 (mt0) cc_final: 0.7511 (mp10) REVERT: s 631 ILE cc_start: 0.9602 (mt) cc_final: 0.9310 (tt) REVERT: t 29 SER cc_start: 0.9273 (m) cc_final: 0.8795 (t) REVERT: t 92 SER cc_start: 0.8772 (t) cc_final: 0.8483 (m) REVERT: t 228 GLN cc_start: 0.8397 (mp-120) cc_final: 0.8130 (mp10) REVERT: t 255 SER cc_start: 0.9307 (m) cc_final: 0.8914 (p) REVERT: t 272 ASP cc_start: 0.8755 (t0) cc_final: 0.7960 (t0) REVERT: t 283 ARG cc_start: 0.8300 (ttt90) cc_final: 0.7756 (tpp-160) REVERT: t 326 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7672 (mm-30) REVERT: t 348 ILE cc_start: 0.8400 (mt) cc_final: 0.8200 (tt) REVERT: t 367 ILE cc_start: 0.9082 (mp) cc_final: 0.8662 (mm) REVERT: t 400 ILE cc_start: 0.8839 (mt) cc_final: 0.8637 (mt) REVERT: t 430 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8362 (mt) REVERT: t 567 ASN cc_start: 0.7761 (m-40) cc_final: 0.7522 (m-40) REVERT: t 570 ASN cc_start: 0.7814 (m-40) cc_final: 0.7143 (m-40) REVERT: t 594 MET cc_start: 0.8448 (tpp) cc_final: 0.8214 (tpp) REVERT: t 721 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6709 (tm-30) REVERT: u 29 SER cc_start: 0.9123 (m) cc_final: 0.8744 (t) REVERT: u 115 ASP cc_start: 0.7457 (m-30) cc_final: 0.7094 (m-30) REVERT: u 283 ARG cc_start: 0.8281 (ttt90) cc_final: 0.7727 (ttt90) REVERT: u 336 ASP cc_start: 0.7636 (p0) cc_final: 0.7354 (p0) REVERT: u 352 PHE cc_start: 0.8274 (m-80) cc_final: 0.7891 (m-80) REVERT: u 414 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8487 (tm) REVERT: u 416 TRP cc_start: 0.9003 (m-10) cc_final: 0.8716 (m-10) REVERT: u 417 SER cc_start: 0.9106 (m) cc_final: 0.8748 (t) REVERT: u 534 GLU cc_start: 0.8850 (pp20) cc_final: 0.8520 (pp20) REVERT: u 567 ASN cc_start: 0.8072 (m-40) cc_final: 0.7864 (m-40) REVERT: u 594 MET cc_start: 0.8373 (tpp) cc_final: 0.8119 (tpp) REVERT: u 697 ASP cc_start: 0.7507 (p0) cc_final: 0.7210 (p0) REVERT: v 283 ARG cc_start: 0.8264 (ttt90) cc_final: 0.7604 (tpp-160) REVERT: v 308 MET cc_start: 0.8663 (mmm) cc_final: 0.8149 (mmm) REVERT: v 314 ARG cc_start: 0.7872 (ttt90) cc_final: 0.7574 (tpt-90) REVERT: v 364 GLU cc_start: 0.7382 (mp0) cc_final: 0.7039 (pm20) REVERT: v 403 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7982 (tt) REVERT: v 417 SER cc_start: 0.8882 (m) cc_final: 0.8400 (t) REVERT: v 644 GLU cc_start: 0.6610 (tm-30) cc_final: 0.6051 (tm-30) REVERT: v 666 MET cc_start: 0.7812 (ppp) cc_final: 0.7442 (ppp) REVERT: v 703 LEU cc_start: 0.8435 (tt) cc_final: 0.8202 (tt) REVERT: v 742 ARG cc_start: 0.8234 (mmt180) cc_final: 0.7589 (mmp-170) REVERT: w 29 SER cc_start: 0.9253 (m) cc_final: 0.8888 (t) REVERT: w 115 ASP cc_start: 0.7561 (m-30) cc_final: 0.7288 (m-30) REVERT: w 178 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8193 (ttmm) REVERT: w 255 SER cc_start: 0.9185 (m) cc_final: 0.8717 (p) REVERT: w 272 ASP cc_start: 0.8797 (t0) cc_final: 0.8203 (t0) REVERT: w 308 MET cc_start: 0.8618 (mmm) cc_final: 0.7841 (mmm) REVERT: w 325 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7381 (pp) REVERT: w 367 ILE cc_start: 0.9018 (mp) cc_final: 0.8602 (mm) REVERT: w 416 TRP cc_start: 0.8930 (m-10) cc_final: 0.8679 (m-10) REVERT: w 567 ASN cc_start: 0.7756 (m-40) cc_final: 0.7452 (m-40) REVERT: w 594 MET cc_start: 0.8287 (tpp) cc_final: 0.8056 (tpp) REVERT: x 308 MET cc_start: 0.8822 (mmm) cc_final: 0.8540 (mmm) REVERT: x 416 TRP cc_start: 0.9004 (m-10) cc_final: 0.8413 (m-10) REVERT: x 417 SER cc_start: 0.8943 (m) cc_final: 0.8402 (t) REVERT: x 477 GLN cc_start: 0.7500 (mt0) cc_final: 0.7072 (mt0) REVERT: x 550 GLN cc_start: 0.8423 (mt0) cc_final: 0.7942 (mp10) REVERT: x 561 MET cc_start: 0.8007 (tpp) cc_final: 0.7661 (ttt) REVERT: x 697 ASP cc_start: 0.7779 (p0) cc_final: 0.7504 (p0) REVERT: x 726 ASN cc_start: 0.7931 (m110) cc_final: 0.7723 (m-40) outliers start: 155 outliers final: 72 residues processed: 676 average time/residue: 0.2282 time to fit residues: 254.3381 Evaluate side-chains 547 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 468 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 78 TYR Chi-restraints excluded: chain s residue 138 THR Chi-restraints excluded: chain s residue 290 VAL Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 335 VAL Chi-restraints excluded: chain s residue 350 ASP Chi-restraints excluded: chain s residue 368 LEU Chi-restraints excluded: chain s residue 395 VAL Chi-restraints excluded: chain s residue 403 LEU Chi-restraints excluded: chain s residue 407 VAL Chi-restraints excluded: chain s residue 412 GLU Chi-restraints excluded: chain s residue 423 VAL Chi-restraints excluded: chain s residue 492 VAL Chi-restraints excluded: chain s residue 770 SER Chi-restraints excluded: chain t residue 26 ASP Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 223 THR Chi-restraints excluded: chain t residue 352 PHE Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 403 LEU Chi-restraints excluded: chain t residue 414 LEU Chi-restraints excluded: chain t residue 423 VAL Chi-restraints excluded: chain t residue 430 LEU Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 531 LEU Chi-restraints excluded: chain u residue 26 ASP Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 223 THR Chi-restraints excluded: chain u residue 297 TRP Chi-restraints excluded: chain u residue 335 VAL Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 403 LEU Chi-restraints excluded: chain u residue 414 LEU Chi-restraints excluded: chain u residue 445 VAL Chi-restraints excluded: chain u residue 730 THR Chi-restraints excluded: chain u residue 770 SER Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 151 ASP Chi-restraints excluded: chain v residue 223 THR Chi-restraints excluded: chain v residue 325 LEU Chi-restraints excluded: chain v residue 335 VAL Chi-restraints excluded: chain v residue 395 VAL Chi-restraints excluded: chain v residue 403 LEU Chi-restraints excluded: chain v residue 430 LEU Chi-restraints excluded: chain v residue 431 THR Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 572 PHE Chi-restraints excluded: chain v residue 604 SER Chi-restraints excluded: chain v residue 661 ASN Chi-restraints excluded: chain w residue 26 ASP Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 78 TYR Chi-restraints excluded: chain w residue 178 LYS Chi-restraints excluded: chain w residue 219 PHE Chi-restraints excluded: chain w residue 223 THR Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 403 LEU Chi-restraints excluded: chain w residue 423 VAL Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 770 SER Chi-restraints excluded: chain w residue 781 CYS Chi-restraints excluded: chain x residue 49 VAL Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 290 VAL Chi-restraints excluded: chain x residue 346 SER Chi-restraints excluded: chain x residue 395 VAL Chi-restraints excluded: chain x residue 403 LEU Chi-restraints excluded: chain x residue 414 LEU Chi-restraints excluded: chain x residue 492 VAL Chi-restraints excluded: chain x residue 572 PHE Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 730 THR Chi-restraints excluded: chain x residue 781 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 32 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 334 optimal weight: 10.0000 chunk 333 optimal weight: 9.9990 chunk 465 optimal weight: 2.9990 chunk 276 optimal weight: 10.0000 chunk 312 optimal weight: 0.7980 chunk 456 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 355 optimal weight: 0.0070 chunk 353 optimal weight: 4.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 150 GLN ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 446 GLN s 491 HIS s 538 GLN t 76 GLN t 150 GLN ** t 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 302 GLN ** t 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 672 ASN u 67 HIS u 421 GLN u 491 HIS u 538 GLN v 31 GLN v 150 GLN ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 532 ASN ** v 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 10 ASN w 187 HIS ** x 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 150 GLN x 491 HIS x 538 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.120027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.091961 restraints weight = 74389.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.094142 restraints weight = 40891.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.095536 restraints weight = 27512.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.096429 restraints weight = 21180.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.096986 restraints weight = 17837.868| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 38748 Z= 0.167 Angle : 0.916 16.527 52692 Z= 0.462 Chirality : 0.053 0.202 5640 Planarity : 0.005 0.070 6918 Dihedral : 8.740 55.909 5216 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.53 % Allowed : 16.94 % Favored : 82.53 % Rotamer: Outliers : 4.37 % Allowed : 17.08 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.33 % Twisted Proline : 2.78 % Twisted General : 1.51 % 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: -4.20 (0.11), residues: 4716 helix: -2.98 (0.41), residues: 90 sheet: -2.57 (0.13), residues: 1572 loop : -3.06 (0.10), residues: 3054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG x 628 TYR 0.028 0.002 TYR v 405 PHE 0.033 0.002 PHE s 50 TRP 0.024 0.002 TRP t 195 HIS 0.009 0.002 HIS s 249 Details of bonding type rmsd covalent geometry : bond 0.00372 (38748) covalent geometry : angle 0.91596 (52692) hydrogen bonds : bond 0.03531 ( 661) hydrogen bonds : angle 7.18562 ( 1605) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 535 time to evaluate : 1.391 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: s 29 SER cc_start: 0.9074 (m) cc_final: 0.8347 (t) REVERT: s 75 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6600 (mm-30) REVERT: s 78 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7127 (t80) REVERT: s 266 MET cc_start: 0.8351 (mtt) cc_final: 0.8124 (ttm) REVERT: s 308 MET cc_start: 0.8800 (mmm) cc_final: 0.8353 (mtm) REVERT: s 364 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6303 (pm20) REVERT: s 367 ILE cc_start: 0.9231 (mp) cc_final: 0.8937 (mm) REVERT: s 403 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7943 (tt) REVERT: s 591 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7659 (tpt170) REVERT: t 29 SER cc_start: 0.9219 (m) cc_final: 0.8807 (t) REVERT: t 78 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.6561 (t80) REVERT: t 92 SER cc_start: 0.8755 (t) cc_final: 0.8553 (m) REVERT: t 228 GLN cc_start: 0.8468 (mp-120) cc_final: 0.8258 (mp10) REVERT: t 255 SER cc_start: 0.9237 (m) cc_final: 0.8851 (p) REVERT: t 272 ASP cc_start: 0.8612 (t0) cc_final: 0.8004 (t0) REVERT: t 283 ARG cc_start: 0.8270 (ttt90) cc_final: 0.7972 (tpp-160) REVERT: t 308 MET cc_start: 0.8491 (mmm) cc_final: 0.7748 (mmm) REVERT: t 348 ILE cc_start: 0.8444 (mt) cc_final: 0.8184 (tt) REVERT: t 360 PHE cc_start: 0.8633 (m-10) cc_final: 0.8289 (m-10) REVERT: t 367 ILE cc_start: 0.9120 (mp) cc_final: 0.8671 (mm) REVERT: t 417 SER cc_start: 0.9138 (m) cc_final: 0.8696 (t) REVERT: t 430 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8263 (mt) REVERT: t 591 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7682 (tpt90) REVERT: t 697 ASP cc_start: 0.6330 (p0) cc_final: 0.6052 (p0) REVERT: t 701 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8879 (tp) REVERT: t 728 LYS cc_start: 0.8820 (tmmt) cc_final: 0.8586 (tttp) REVERT: u 29 SER cc_start: 0.9105 (m) cc_final: 0.8747 (t) REVERT: u 115 ASP cc_start: 0.7342 (m-30) cc_final: 0.6834 (m-30) REVERT: u 283 ARG cc_start: 0.8198 (ttt90) cc_final: 0.7813 (ttt90) REVERT: u 332 CYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6440 (p) REVERT: u 336 ASP cc_start: 0.7550 (p0) cc_final: 0.7335 (p0) REVERT: u 352 PHE cc_start: 0.8220 (m-80) cc_final: 0.7942 (m-80) REVERT: u 387 ASP cc_start: 0.7653 (t0) cc_final: 0.7286 (t0) REVERT: u 477 GLN cc_start: 0.8168 (mt0) cc_final: 0.7856 (mm-40) REVERT: u 486 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7313 (tt0) REVERT: u 550 GLN cc_start: 0.8335 (mt0) cc_final: 0.7883 (mp10) REVERT: u 561 MET cc_start: 0.8300 (tpp) cc_final: 0.7936 (ttt) REVERT: u 591 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7798 (tpt170) REVERT: u 697 ASP cc_start: 0.7404 (p0) cc_final: 0.7151 (p0) REVERT: u 730 THR cc_start: 0.8013 (m) cc_final: 0.7599 (t) REVERT: v 308 MET cc_start: 0.8655 (mmm) cc_final: 0.8231 (mmm) REVERT: v 364 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6870 (pm20) REVERT: v 403 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8280 (tt) REVERT: v 416 TRP cc_start: 0.9059 (m-10) cc_final: 0.8857 (m-10) REVERT: v 417 SER cc_start: 0.8742 (m) cc_final: 0.8386 (t) REVERT: v 492 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.8963 (p) REVERT: v 533 GLU cc_start: 0.8809 (pm20) cc_final: 0.8346 (pm20) REVERT: v 591 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.6866 (tpt90) REVERT: v 644 GLU cc_start: 0.6553 (tm-30) cc_final: 0.5845 (tm-30) REVERT: v 703 LEU cc_start: 0.8574 (tt) cc_final: 0.8370 (tt) REVERT: v 712 ASN cc_start: 0.7956 (t0) cc_final: 0.7750 (t0) REVERT: v 742 ARG cc_start: 0.8116 (mmt180) cc_final: 0.7747 (mmp-170) REVERT: w 29 SER cc_start: 0.9230 (m) cc_final: 0.8898 (t) REVERT: w 51 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8974 (pp) REVERT: w 115 ASP cc_start: 0.7502 (m-30) cc_final: 0.7207 (m-30) REVERT: w 168 HIS cc_start: 0.8559 (t-170) cc_final: 0.8195 (t70) REVERT: w 255 SER cc_start: 0.9204 (m) cc_final: 0.8782 (p) REVERT: w 272 ASP cc_start: 0.8631 (t0) cc_final: 0.7915 (t0) REVERT: w 308 MET cc_start: 0.8498 (mmm) cc_final: 0.7750 (mmm) REVERT: w 325 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7377 (pp) REVERT: w 367 ILE cc_start: 0.9051 (mp) cc_final: 0.8613 (mm) REVERT: w 417 SER cc_start: 0.9037 (m) cc_final: 0.8670 (t) REVERT: w 477 GLN cc_start: 0.7432 (mt0) cc_final: 0.7035 (mt0) REVERT: w 567 ASN cc_start: 0.7877 (m-40) cc_final: 0.7657 (m-40) REVERT: w 701 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.8913 (tp) REVERT: x 9 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7893 (mmtm) REVERT: x 29 SER cc_start: 0.9185 (m) cc_final: 0.8873 (t) REVERT: x 115 ASP cc_start: 0.7629 (m-30) cc_final: 0.7330 (m-30) REVERT: x 413 LEU cc_start: 0.8932 (tt) cc_final: 0.8644 (tp) REVERT: x 417 SER cc_start: 0.8946 (m) cc_final: 0.8556 (t) REVERT: x 477 GLN cc_start: 0.7582 (mt0) cc_final: 0.7211 (mt0) REVERT: x 535 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8815 (tp) REVERT: x 550 GLN cc_start: 0.8378 (mt0) cc_final: 0.7908 (mp10) REVERT: x 561 MET cc_start: 0.8187 (tpp) cc_final: 0.7903 (ttt) REVERT: x 591 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7929 (tpt170) REVERT: x 697 ASP cc_start: 0.7497 (p0) cc_final: 0.7267 (p0) REVERT: x 726 ASN cc_start: 0.7822 (m110) cc_final: 0.7607 (m-40) REVERT: x 730 THR cc_start: 0.8216 (m) cc_final: 0.7944 (t) outliers start: 180 outliers final: 92 residues processed: 671 average time/residue: 0.2262 time to fit residues: 248.6025 Evaluate side-chains 576 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 465 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 42 LEU Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 78 TYR Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 290 VAL Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 335 VAL Chi-restraints excluded: chain s residue 350 ASP Chi-restraints excluded: chain s residue 364 GLU Chi-restraints excluded: chain s residue 395 VAL Chi-restraints excluded: chain s residue 403 LEU Chi-restraints excluded: chain s residue 412 GLU Chi-restraints excluded: chain s residue 446 GLN Chi-restraints excluded: chain s residue 492 VAL Chi-restraints excluded: chain s residue 535 LEU Chi-restraints excluded: chain s residue 572 PHE Chi-restraints excluded: chain s residue 591 ARG Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain s residue 718 ILE Chi-restraints excluded: chain s residue 730 THR Chi-restraints excluded: chain t residue 42 LEU Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 78 TYR Chi-restraints excluded: chain t residue 223 THR Chi-restraints excluded: chain t residue 253 SER Chi-restraints excluded: chain t residue 270 VAL Chi-restraints excluded: chain t residue 352 PHE Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 403 LEU Chi-restraints excluded: chain t residue 405 TYR Chi-restraints excluded: chain t residue 414 LEU Chi-restraints excluded: chain t residue 423 VAL Chi-restraints excluded: chain t residue 430 LEU Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 535 LEU Chi-restraints excluded: chain t residue 591 ARG Chi-restraints excluded: chain t residue 596 MET Chi-restraints excluded: chain t residue 673 ILE Chi-restraints excluded: chain t residue 701 LEU Chi-restraints excluded: chain u residue 22 LEU Chi-restraints excluded: chain u residue 42 LEU Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 297 TRP Chi-restraints excluded: chain u residue 332 CYS Chi-restraints excluded: chain u residue 344 VAL Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 395 VAL Chi-restraints excluded: chain u residue 405 TYR Chi-restraints excluded: chain u residue 445 VAL Chi-restraints excluded: chain u residue 492 VAL Chi-restraints excluded: chain u residue 591 ARG Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 138 THR Chi-restraints excluded: chain v residue 151 ASP Chi-restraints excluded: chain v residue 223 THR Chi-restraints excluded: chain v residue 290 VAL Chi-restraints excluded: chain v residue 325 LEU Chi-restraints excluded: chain v residue 335 VAL Chi-restraints excluded: chain v residue 348 ILE Chi-restraints excluded: chain v residue 350 ASP Chi-restraints excluded: chain v residue 364 GLU Chi-restraints excluded: chain v residue 395 VAL Chi-restraints excluded: chain v residue 403 LEU Chi-restraints excluded: chain v residue 405 TYR Chi-restraints excluded: chain v residue 430 LEU Chi-restraints excluded: chain v residue 431 THR Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 492 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 591 ARG Chi-restraints excluded: chain v residue 687 THR Chi-restraints excluded: chain v residue 718 ILE Chi-restraints excluded: chain v residue 792 SER Chi-restraints excluded: chain w residue 26 ASP Chi-restraints excluded: chain w residue 42 LEU Chi-restraints excluded: chain w residue 51 LEU Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 78 TYR Chi-restraints excluded: chain w residue 219 PHE Chi-restraints excluded: chain w residue 223 THR Chi-restraints excluded: chain w residue 253 SER Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 403 LEU Chi-restraints excluded: chain w residue 414 LEU Chi-restraints excluded: chain w residue 423 VAL Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 585 LEU Chi-restraints excluded: chain w residue 591 ARG Chi-restraints excluded: chain w residue 647 THR Chi-restraints excluded: chain w residue 673 ILE Chi-restraints excluded: chain w residue 687 THR Chi-restraints excluded: chain w residue 701 LEU Chi-restraints excluded: chain w residue 703 LEU Chi-restraints excluded: chain w residue 781 CYS Chi-restraints excluded: chain x residue 49 VAL Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 290 VAL Chi-restraints excluded: chain x residue 304 LEU Chi-restraints excluded: chain x residue 364 GLU Chi-restraints excluded: chain x residue 395 VAL Chi-restraints excluded: chain x residue 403 LEU Chi-restraints excluded: chain x residue 414 LEU Chi-restraints excluded: chain x residue 535 LEU Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 781 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 39 optimal weight: 0.0970 chunk 359 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 chunk 322 optimal weight: 3.9990 chunk 425 optimal weight: 2.9990 chunk 444 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 437 optimal weight: 4.9990 chunk 367 optimal weight: 2.9990 chunk 446 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 10 ASN ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 43 GLN s 150 GLN ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 302 GLN ** t 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 76 GLN u 150 GLN u 229 GLN u 252 GLN u 260 ASN u 421 GLN ** u 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 43 GLN v 62 GLN v 150 GLN ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 10 ASN ** w 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 43 GLN x 260 ASN ** x 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.085717 restraints weight = 75556.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.087927 restraints weight = 40459.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.089334 restraints weight = 26870.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.090222 restraints weight = 20546.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.090776 restraints weight = 17296.717| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 38748 Z= 0.261 Angle : 0.957 15.837 52692 Z= 0.484 Chirality : 0.054 0.220 5640 Planarity : 0.005 0.072 6918 Dihedral : 8.607 59.324 5216 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.51 % Allowed : 17.98 % Favored : 81.51 % Rotamer: Outliers : 4.44 % Allowed : 18.10 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.33 % Twisted Proline : 2.78 % Twisted General : 1.29 % 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: -4.14 (0.11), residues: 4716 helix: -2.80 (0.42), residues: 96 sheet: -2.49 (0.13), residues: 1536 loop : -3.05 (0.10), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG w 283 TYR 0.023 0.002 TYR v 77 PHE 0.022 0.002 PHE s 352 TRP 0.025 0.002 TRP s 416 HIS 0.009 0.002 HIS t 249 Details of bonding type rmsd covalent geometry : bond 0.00602 (38748) covalent geometry : angle 0.95698 (52692) hydrogen bonds : bond 0.03662 ( 661) hydrogen bonds : angle 7.18270 ( 1605) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 481 time to evaluate : 1.387 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: s 29 SER cc_start: 0.9196 (m) cc_final: 0.8479 (t) REVERT: s 78 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.7291 (t80) REVERT: s 283 ARG cc_start: 0.8353 (ttt90) cc_final: 0.8028 (tpp-160) REVERT: s 308 MET cc_start: 0.8825 (mmm) cc_final: 0.8374 (mtm) REVERT: s 332 CYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7152 (p) REVERT: s 364 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6572 (pm20) REVERT: s 367 ILE cc_start: 0.9308 (mp) cc_final: 0.9027 (mm) REVERT: s 417 SER cc_start: 0.9054 (m) cc_final: 0.8663 (t) REVERT: s 591 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7792 (tpt170) REVERT: t 29 SER cc_start: 0.9293 (m) cc_final: 0.9029 (t) REVERT: t 77 TYR cc_start: 0.6893 (m-10) cc_final: 0.6632 (m-10) REVERT: t 78 TYR cc_start: 0.8707 (OUTLIER) cc_final: 0.6576 (t80) REVERT: t 92 SER cc_start: 0.8834 (t) cc_final: 0.8582 (m) REVERT: t 255 SER cc_start: 0.9317 (m) cc_final: 0.8937 (p) REVERT: t 272 ASP cc_start: 0.8821 (t0) cc_final: 0.8228 (t0) REVERT: t 283 ARG cc_start: 0.8291 (ttt90) cc_final: 0.7993 (ttt90) REVERT: t 308 MET cc_start: 0.8699 (mmm) cc_final: 0.8282 (mmm) REVERT: t 314 ARG cc_start: 0.8242 (tpt-90) cc_final: 0.7988 (tpt-90) REVERT: t 325 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7742 (pp) REVERT: t 367 ILE cc_start: 0.9236 (mp) cc_final: 0.8806 (mm) REVERT: t 417 SER cc_start: 0.9093 (m) cc_final: 0.8784 (t) REVERT: t 430 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8417 (mt) REVERT: t 567 ASN cc_start: 0.7673 (m-40) cc_final: 0.7414 (m-40) REVERT: t 697 ASP cc_start: 0.6848 (p0) cc_final: 0.6555 (p0) REVERT: t 721 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6975 (tm-30) REVERT: u 29 SER cc_start: 0.9218 (m) cc_final: 0.8885 (t) REVERT: u 115 ASP cc_start: 0.7538 (m-30) cc_final: 0.7025 (m-30) REVERT: u 283 ARG cc_start: 0.8229 (ttt90) cc_final: 0.7817 (ttt90) REVERT: u 477 GLN cc_start: 0.8264 (mt0) cc_final: 0.7979 (mm-40) REVERT: u 486 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7248 (tt0) REVERT: u 525 MET cc_start: 0.8688 (tpp) cc_final: 0.8251 (tpp) REVERT: u 534 GLU cc_start: 0.9047 (pp20) cc_final: 0.8817 (pp20) REVERT: u 550 GLN cc_start: 0.8519 (mt0) cc_final: 0.7964 (mp10) REVERT: u 561 MET cc_start: 0.8519 (tpp) cc_final: 0.8105 (ttt) REVERT: u 644 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6986 (mm-30) REVERT: u 697 ASP cc_start: 0.7533 (p0) cc_final: 0.7247 (p0) REVERT: v 77 TYR cc_start: 0.7048 (m-10) cc_final: 0.6821 (m-10) REVERT: v 115 ASP cc_start: 0.7730 (m-30) cc_final: 0.7427 (m-30) REVERT: v 308 MET cc_start: 0.8888 (mmm) cc_final: 0.8370 (mtm) REVERT: v 332 CYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7662 (p) REVERT: v 364 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: v 644 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6243 (tm-30) REVERT: v 666 MET cc_start: 0.7726 (ppp) cc_final: 0.6991 (ppp) REVERT: v 742 ARG cc_start: 0.8396 (mmt180) cc_final: 0.8077 (mmp-170) REVERT: w 29 SER cc_start: 0.9315 (m) cc_final: 0.9029 (t) REVERT: w 51 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8992 (pp) REVERT: w 115 ASP cc_start: 0.7724 (m-30) cc_final: 0.7339 (m-30) REVERT: w 272 ASP cc_start: 0.8582 (t0) cc_final: 0.7916 (t0) REVERT: w 283 ARG cc_start: 0.8338 (ttt90) cc_final: 0.7960 (tpp-160) REVERT: w 308 MET cc_start: 0.8803 (mmm) cc_final: 0.8318 (mmm) REVERT: w 325 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7505 (pp) REVERT: w 364 GLU cc_start: 0.6742 (pm20) cc_final: 0.6278 (pm20) REVERT: w 367 ILE cc_start: 0.9129 (mp) cc_final: 0.8698 (mm) REVERT: w 570 ASN cc_start: 0.8283 (m-40) cc_final: 0.7774 (m-40) REVERT: w 591 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8052 (tpt90) REVERT: w 632 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8930 (p) REVERT: w 731 MET cc_start: 0.8704 (tmm) cc_final: 0.7815 (tmm) REVERT: x 29 SER cc_start: 0.9237 (m) cc_final: 0.8876 (t) REVERT: x 272 ASP cc_start: 0.9315 (t70) cc_final: 0.8547 (t0) REVERT: x 283 ARG cc_start: 0.8346 (ttt90) cc_final: 0.8065 (ttt90) REVERT: x 325 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7133 (pp) REVERT: x 477 GLN cc_start: 0.7686 (mt0) cc_final: 0.7362 (mt0) REVERT: x 561 MET cc_start: 0.8491 (tpp) cc_final: 0.8005 (ttt) REVERT: x 591 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7684 (tpt170) REVERT: x 697 ASP cc_start: 0.7282 (p0) cc_final: 0.7028 (p0) REVERT: x 730 THR cc_start: 0.8450 (m) cc_final: 0.8209 (t) outliers start: 183 outliers final: 104 residues processed: 622 average time/residue: 0.2237 time to fit residues: 228.9229 Evaluate side-chains 548 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 429 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 78 TYR Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 290 VAL Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 332 CYS Chi-restraints excluded: chain s residue 335 VAL Chi-restraints excluded: chain s residue 350 ASP Chi-restraints excluded: chain s residue 351 VAL Chi-restraints excluded: chain s residue 364 GLU Chi-restraints excluded: chain s residue 395 VAL Chi-restraints excluded: chain s residue 405 TYR Chi-restraints excluded: chain s residue 412 GLU Chi-restraints excluded: chain s residue 492 VAL Chi-restraints excluded: chain s residue 572 PHE Chi-restraints excluded: chain s residue 591 ARG Chi-restraints excluded: chain s residue 673 ILE Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 78 TYR Chi-restraints excluded: chain t residue 219 PHE Chi-restraints excluded: chain t residue 223 THR Chi-restraints excluded: chain t residue 253 SER Chi-restraints excluded: chain t residue 270 VAL Chi-restraints excluded: chain t residue 325 LEU Chi-restraints excluded: chain t residue 350 ASP Chi-restraints excluded: chain t residue 352 PHE Chi-restraints excluded: chain t residue 393 VAL Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 405 TYR Chi-restraints excluded: chain t residue 414 LEU Chi-restraints excluded: chain t residue 423 VAL Chi-restraints excluded: chain t residue 430 LEU Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 535 LEU Chi-restraints excluded: chain t residue 596 MET Chi-restraints excluded: chain t residue 667 VAL Chi-restraints excluded: chain t residue 673 ILE Chi-restraints excluded: chain u residue 22 LEU Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 86 ILE Chi-restraints excluded: chain u residue 138 THR Chi-restraints excluded: chain u residue 223 THR Chi-restraints excluded: chain u residue 247 VAL Chi-restraints excluded: chain u residue 297 TRP Chi-restraints excluded: chain u residue 304 LEU Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 395 VAL Chi-restraints excluded: chain u residue 403 LEU Chi-restraints excluded: chain u residue 405 TYR Chi-restraints excluded: chain u residue 441 THR Chi-restraints excluded: chain u residue 445 VAL Chi-restraints excluded: chain u residue 492 VAL Chi-restraints excluded: chain u residue 542 HIS Chi-restraints excluded: chain u residue 718 ILE Chi-restraints excluded: chain u residue 792 SER Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 138 THR Chi-restraints excluded: chain v residue 223 THR Chi-restraints excluded: chain v residue 290 VAL Chi-restraints excluded: chain v residue 332 CYS Chi-restraints excluded: chain v residue 335 VAL Chi-restraints excluded: chain v residue 348 ILE Chi-restraints excluded: chain v residue 350 ASP Chi-restraints excluded: chain v residue 364 GLU Chi-restraints excluded: chain v residue 395 VAL Chi-restraints excluded: chain v residue 405 TYR Chi-restraints excluded: chain v residue 430 LEU Chi-restraints excluded: chain v residue 431 THR Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 542 HIS Chi-restraints excluded: chain v residue 572 PHE Chi-restraints excluded: chain v residue 673 ILE Chi-restraints excluded: chain v residue 718 ILE Chi-restraints excluded: chain v residue 725 SER Chi-restraints excluded: chain v residue 769 LEU Chi-restraints excluded: chain v residue 781 CYS Chi-restraints excluded: chain v residue 792 SER Chi-restraints excluded: chain w residue 51 LEU Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 78 TYR Chi-restraints excluded: chain w residue 92 SER Chi-restraints excluded: chain w residue 219 PHE Chi-restraints excluded: chain w residue 223 THR Chi-restraints excluded: chain w residue 253 SER Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 414 LEU Chi-restraints excluded: chain w residue 423 VAL Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 585 LEU Chi-restraints excluded: chain w residue 591 ARG Chi-restraints excluded: chain w residue 632 THR Chi-restraints excluded: chain w residue 673 ILE Chi-restraints excluded: chain w residue 687 THR Chi-restraints excluded: chain w residue 703 LEU Chi-restraints excluded: chain w residue 774 THR Chi-restraints excluded: chain w residue 781 CYS Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 138 THR Chi-restraints excluded: chain x residue 219 PHE Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 290 VAL Chi-restraints excluded: chain x residue 304 LEU Chi-restraints excluded: chain x residue 325 LEU Chi-restraints excluded: chain x residue 364 GLU Chi-restraints excluded: chain x residue 395 VAL Chi-restraints excluded: chain x residue 407 VAL Chi-restraints excluded: chain x residue 535 LEU Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 684 ILE Chi-restraints excluded: chain x residue 703 LEU Chi-restraints excluded: chain x residue 718 ILE Chi-restraints excluded: chain x residue 781 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 363 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 289 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 447 optimal weight: 1.9990 chunk 255 optimal weight: 10.0000 chunk 456 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 617 HIS ** t 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 43 GLN u 67 HIS ** u 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 661 ASN ** v 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 150 GLN ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 532 ASN v 538 GLN ** v 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 31 GLN ** x 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 726 ASN ** x 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.113734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.084865 restraints weight = 75730.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.087064 restraints weight = 40311.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.088473 restraints weight = 26744.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.089358 restraints weight = 20453.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.089917 restraints weight = 17185.546| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 38748 Z= 0.249 Angle : 0.943 16.298 52692 Z= 0.478 Chirality : 0.054 0.209 5640 Planarity : 0.005 0.069 6918 Dihedral : 8.472 57.867 5216 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.49 % Allowed : 17.45 % Favored : 82.06 % Rotamer: Outliers : 4.71 % Allowed : 18.56 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.33 % Twisted Proline : 2.78 % Twisted General : 1.11 % 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: -4.10 (0.11), residues: 4716 helix: -2.14 (0.42), residues: 132 sheet: -2.52 (0.13), residues: 1554 loop : -3.00 (0.10), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG u 628 TYR 0.016 0.002 TYR u 767 PHE 0.039 0.002 PHE u 352 TRP 0.047 0.002 TRP u 416 HIS 0.009 0.002 HIS t 249 Details of bonding type rmsd covalent geometry : bond 0.00576 (38748) covalent geometry : angle 0.94297 (52692) hydrogen bonds : bond 0.03572 ( 661) hydrogen bonds : angle 7.10158 ( 1605) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 469 time to evaluate : 1.538 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: s 29 SER cc_start: 0.9233 (m) cc_final: 0.8605 (t) REVERT: s 78 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.7380 (t80) REVERT: s 283 ARG cc_start: 0.8259 (ttt90) cc_final: 0.7831 (ttt90) REVERT: s 308 MET cc_start: 0.8897 (mmm) cc_final: 0.8477 (mtm) REVERT: s 352 PHE cc_start: 0.8261 (m-80) cc_final: 0.7945 (m-80) REVERT: s 364 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: s 550 GLN cc_start: 0.8237 (mt0) cc_final: 0.7906 (mp10) REVERT: s 632 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8813 (p) REVERT: s 666 MET cc_start: 0.7741 (ppp) cc_final: 0.7514 (ppp) REVERT: t 29 SER cc_start: 0.9367 (m) cc_final: 0.9087 (t) REVERT: t 78 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.6822 (t80) REVERT: t 92 SER cc_start: 0.8856 (t) cc_final: 0.8581 (m) REVERT: t 272 ASP cc_start: 0.8739 (t0) cc_final: 0.8187 (t0) REVERT: t 283 ARG cc_start: 0.8285 (ttt90) cc_final: 0.8059 (ttt90) REVERT: t 308 MET cc_start: 0.8745 (mmm) cc_final: 0.8276 (mmm) REVERT: t 325 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7855 (pp) REVERT: t 430 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8446 (mt) REVERT: t 457 ASN cc_start: 0.9003 (OUTLIER) cc_final: 0.8709 (m110) REVERT: t 542 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.7727 (m90) REVERT: t 591 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8119 (tpt90) REVERT: t 697 ASP cc_start: 0.6900 (p0) cc_final: 0.6433 (p0) REVERT: t 789 ARG cc_start: 0.9320 (OUTLIER) cc_final: 0.8951 (ptm160) REVERT: u 29 SER cc_start: 0.9227 (m) cc_final: 0.8923 (t) REVERT: u 62 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: u 115 ASP cc_start: 0.7640 (m-30) cc_final: 0.7069 (m-30) REVERT: u 283 ARG cc_start: 0.8358 (ttt90) cc_final: 0.7896 (ttt90) REVERT: u 387 ASP cc_start: 0.7356 (t70) cc_final: 0.7126 (t0) REVERT: u 416 TRP cc_start: 0.9075 (m-10) cc_final: 0.8791 (m-10) REVERT: u 417 SER cc_start: 0.9114 (m) cc_final: 0.8647 (t) REVERT: u 460 PHE cc_start: 0.8895 (m-10) cc_final: 0.8663 (m-10) REVERT: u 486 GLU cc_start: 0.7591 (mm-30) cc_final: 0.6992 (tt0) REVERT: u 525 MET cc_start: 0.8795 (tpp) cc_final: 0.8485 (tpp) REVERT: u 550 GLN cc_start: 0.8575 (mt0) cc_final: 0.7991 (mp10) REVERT: u 591 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7879 (tpt170) REVERT: u 594 MET cc_start: 0.8833 (tpp) cc_final: 0.8471 (tpp) REVERT: u 644 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6968 (mm-30) REVERT: u 697 ASP cc_start: 0.7653 (p0) cc_final: 0.7308 (p0) REVERT: u 730 THR cc_start: 0.8558 (m) cc_final: 0.8320 (t) REVERT: v 29 SER cc_start: 0.9257 (m) cc_final: 0.8815 (t) REVERT: v 115 ASP cc_start: 0.7733 (m-30) cc_final: 0.7286 (m-30) REVERT: v 272 ASP cc_start: 0.9205 (t70) cc_final: 0.8910 (t70) REVERT: v 283 ARG cc_start: 0.8211 (ttt90) cc_final: 0.7988 (tpp-160) REVERT: v 308 MET cc_start: 0.8838 (mmm) cc_final: 0.8429 (mtm) REVERT: v 364 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: v 644 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6429 (tm-30) REVERT: v 742 ARG cc_start: 0.8472 (mmt180) cc_final: 0.8050 (mmp-170) REVERT: w 51 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8930 (pp) REVERT: w 115 ASP cc_start: 0.7795 (m-30) cc_final: 0.7343 (m-30) REVERT: w 272 ASP cc_start: 0.8711 (t0) cc_final: 0.8346 (t70) REVERT: w 283 ARG cc_start: 0.8264 (ttt90) cc_final: 0.7949 (ttt90) REVERT: w 308 MET cc_start: 0.8831 (mmm) cc_final: 0.8288 (mmm) REVERT: w 325 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7530 (pp) REVERT: w 364 GLU cc_start: 0.7074 (pm20) cc_final: 0.6542 (pm20) REVERT: w 367 ILE cc_start: 0.9169 (mp) cc_final: 0.8728 (mm) REVERT: w 591 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.8092 (tpt90) REVERT: w 632 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8962 (p) REVERT: w 701 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9035 (tp) REVERT: w 731 MET cc_start: 0.8778 (tmm) cc_final: 0.7619 (tmm) REVERT: x 29 SER cc_start: 0.9258 (m) cc_final: 0.8949 (t) REVERT: x 115 ASP cc_start: 0.7863 (m-30) cc_final: 0.7455 (m-30) REVERT: x 283 ARG cc_start: 0.8227 (ttt90) cc_final: 0.7980 (ttt90) REVERT: x 325 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7310 (pp) REVERT: x 364 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7274 (pm20) REVERT: x 413 LEU cc_start: 0.8730 (tp) cc_final: 0.7784 (tp) REVERT: x 477 GLN cc_start: 0.7828 (mt0) cc_final: 0.7461 (mt0) REVERT: x 519 ASP cc_start: 0.6906 (p0) cc_final: 0.6683 (p0) REVERT: x 533 GLU cc_start: 0.8955 (pm20) cc_final: 0.8714 (pm20) REVERT: x 561 MET cc_start: 0.8502 (tpp) cc_final: 0.7998 (ttt) REVERT: x 591 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7884 (tpt170) REVERT: x 696 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6815 (mm-30) REVERT: x 730 THR cc_start: 0.8483 (m) cc_final: 0.8245 (t) outliers start: 194 outliers final: 110 residues processed: 626 average time/residue: 0.2285 time to fit residues: 233.7751 Evaluate side-chains 548 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 416 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 42 LEU Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 78 TYR Chi-restraints excluded: chain s residue 138 THR Chi-restraints excluded: chain s residue 200 LEU Chi-restraints excluded: chain s residue 204 MET Chi-restraints excluded: chain s residue 290 VAL Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 335 VAL Chi-restraints excluded: chain s residue 350 ASP Chi-restraints excluded: chain s residue 351 VAL Chi-restraints excluded: chain s residue 364 GLU Chi-restraints excluded: chain s residue 395 VAL Chi-restraints excluded: chain s residue 412 GLU Chi-restraints excluded: chain s residue 445 VAL Chi-restraints excluded: chain s residue 535 LEU Chi-restraints excluded: chain s residue 572 PHE Chi-restraints excluded: chain s residue 632 THR Chi-restraints excluded: chain s residue 673 ILE Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain s residue 769 LEU Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 78 TYR Chi-restraints excluded: chain t residue 219 PHE Chi-restraints excluded: chain t residue 223 THR Chi-restraints excluded: chain t residue 253 SER Chi-restraints excluded: chain t residue 270 VAL Chi-restraints excluded: chain t residue 325 LEU Chi-restraints excluded: chain t residue 344 VAL Chi-restraints excluded: chain t residue 352 PHE Chi-restraints excluded: chain t residue 393 VAL Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 414 LEU Chi-restraints excluded: chain t residue 430 LEU Chi-restraints excluded: chain t residue 457 ASN Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 535 LEU Chi-restraints excluded: chain t residue 542 HIS Chi-restraints excluded: chain t residue 591 ARG Chi-restraints excluded: chain t residue 596 MET Chi-restraints excluded: chain t residue 667 VAL Chi-restraints excluded: chain t residue 673 ILE Chi-restraints excluded: chain t residue 789 ARG Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain u residue 86 ILE Chi-restraints excluded: chain u residue 219 PHE Chi-restraints excluded: chain u residue 223 THR Chi-restraints excluded: chain u residue 247 VAL Chi-restraints excluded: chain u residue 297 TRP Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 395 VAL Chi-restraints excluded: chain u residue 403 LEU Chi-restraints excluded: chain u residue 405 TYR Chi-restraints excluded: chain u residue 445 VAL Chi-restraints excluded: chain u residue 492 VAL Chi-restraints excluded: chain u residue 591 ARG Chi-restraints excluded: chain u residue 667 VAL Chi-restraints excluded: chain u residue 718 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 138 THR Chi-restraints excluded: chain v residue 219 PHE Chi-restraints excluded: chain v residue 223 THR Chi-restraints excluded: chain v residue 290 VAL Chi-restraints excluded: chain v residue 305 TRP Chi-restraints excluded: chain v residue 335 VAL Chi-restraints excluded: chain v residue 348 ILE Chi-restraints excluded: chain v residue 350 ASP Chi-restraints excluded: chain v residue 364 GLU Chi-restraints excluded: chain v residue 375 PHE Chi-restraints excluded: chain v residue 395 VAL Chi-restraints excluded: chain v residue 405 TYR Chi-restraints excluded: chain v residue 417 SER Chi-restraints excluded: chain v residue 430 LEU Chi-restraints excluded: chain v residue 431 THR Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 492 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 542 HIS Chi-restraints excluded: chain v residue 572 PHE Chi-restraints excluded: chain v residue 673 ILE Chi-restraints excluded: chain v residue 687 THR Chi-restraints excluded: chain v residue 718 ILE Chi-restraints excluded: chain v residue 725 SER Chi-restraints excluded: chain v residue 769 LEU Chi-restraints excluded: chain v residue 781 CYS Chi-restraints excluded: chain v residue 792 SER Chi-restraints excluded: chain w residue 51 LEU Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 78 TYR Chi-restraints excluded: chain w residue 92 SER Chi-restraints excluded: chain w residue 121 VAL Chi-restraints excluded: chain w residue 219 PHE Chi-restraints excluded: chain w residue 223 THR Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 403 LEU Chi-restraints excluded: chain w residue 414 LEU Chi-restraints excluded: chain w residue 415 ILE Chi-restraints excluded: chain w residue 423 VAL Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 585 LEU Chi-restraints excluded: chain w residue 591 ARG Chi-restraints excluded: chain w residue 596 MET Chi-restraints excluded: chain w residue 632 THR Chi-restraints excluded: chain w residue 666 MET Chi-restraints excluded: chain w residue 673 ILE Chi-restraints excluded: chain w residue 687 THR Chi-restraints excluded: chain w residue 701 LEU Chi-restraints excluded: chain w residue 703 LEU Chi-restraints excluded: chain w residue 774 THR Chi-restraints excluded: chain w residue 781 CYS Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 219 PHE Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 290 VAL Chi-restraints excluded: chain x residue 304 LEU Chi-restraints excluded: chain x residue 325 LEU Chi-restraints excluded: chain x residue 364 GLU Chi-restraints excluded: chain x residue 395 VAL Chi-restraints excluded: chain x residue 405 TYR Chi-restraints excluded: chain x residue 535 LEU Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 684 ILE Chi-restraints excluded: chain x residue 696 GLU Chi-restraints excluded: chain x residue 718 ILE Chi-restraints excluded: chain x residue 769 LEU Chi-restraints excluded: chain x residue 781 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 221 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 307 optimal weight: 0.6980 chunk 304 optimal weight: 0.9980 chunk 301 optimal weight: 0.4980 chunk 446 optimal weight: 0.7980 chunk 323 optimal weight: 2.9990 chunk 285 optimal weight: 0.3980 chunk 72 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 6 GLN ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 446 GLN ** t 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 67 HIS ** v 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 150 GLN ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 260 ASN ** v 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 532 ASN w 6 GLN ** w 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 567 ASN x 726 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.088535 restraints weight = 75225.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.090745 restraints weight = 40986.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.092131 restraints weight = 27435.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.093010 restraints weight = 21101.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.093531 restraints weight = 17789.266| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 38748 Z= 0.169 Angle : 0.914 15.340 52692 Z= 0.459 Chirality : 0.052 0.242 5640 Planarity : 0.005 0.065 6918 Dihedral : 8.184 54.934 5216 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.42 % Allowed : 17.94 % Favored : 81.64 % Rotamer: Outliers : 3.64 % Allowed : 20.35 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 1.33 % Twisted Proline : 1.39 % Twisted General : 0.91 % 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: -4.03 (0.11), residues: 4716 helix: -2.24 (0.36), residues: 162 sheet: -2.58 (0.13), residues: 1470 loop : -2.90 (0.10), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG u 628 TYR 0.020 0.002 TYR v 77 PHE 0.029 0.002 PHE x 352 TRP 0.037 0.002 TRP u 416 HIS 0.009 0.002 HIS s 249 Details of bonding type rmsd covalent geometry : bond 0.00391 (38748) covalent geometry : angle 0.91445 (52692) hydrogen bonds : bond 0.03352 ( 661) hydrogen bonds : angle 6.97104 ( 1605) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 470 time to evaluate : 1.525 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: s 29 SER cc_start: 0.9171 (m) cc_final: 0.8532 (t) REVERT: s 51 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8407 (pp) REVERT: s 78 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.7429 (t80) REVERT: s 115 ASP cc_start: 0.7830 (m-30) cc_final: 0.7395 (m-30) REVERT: s 266 MET cc_start: 0.7914 (ttm) cc_final: 0.7674 (ttm) REVERT: s 283 ARG cc_start: 0.8295 (ttt90) cc_final: 0.8066 (ttt90) REVERT: s 308 MET cc_start: 0.8794 (mmm) cc_final: 0.8420 (mtm) REVERT: s 352 PHE cc_start: 0.8206 (m-80) cc_final: 0.7868 (m-80) REVERT: s 364 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6878 (pm20) REVERT: s 550 GLN cc_start: 0.8063 (mt0) cc_final: 0.7632 (mp10) REVERT: s 596 MET cc_start: 0.7654 (ttp) cc_final: 0.7323 (tpp) REVERT: s 666 MET cc_start: 0.7614 (ppp) cc_final: 0.7367 (ppp) REVERT: t 29 SER cc_start: 0.9307 (m) cc_final: 0.9087 (t) REVERT: t 51 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8808 (pp) REVERT: t 78 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.6475 (t80) REVERT: t 92 SER cc_start: 0.8771 (t) cc_final: 0.8476 (m) REVERT: t 115 ASP cc_start: 0.7730 (m-30) cc_final: 0.7314 (m-30) REVERT: t 272 ASP cc_start: 0.8630 (t0) cc_final: 0.8143 (t0) REVERT: t 308 MET cc_start: 0.8637 (mmm) cc_final: 0.8239 (mmm) REVERT: t 367 ILE cc_start: 0.9236 (mp) cc_final: 0.8766 (mm) REVERT: t 430 LEU cc_start: 0.8577 (mt) cc_final: 0.8348 (mt) REVERT: t 457 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8624 (m110) REVERT: t 674 ASN cc_start: 0.7904 (t0) cc_final: 0.7664 (p0) REVERT: t 697 ASP cc_start: 0.6797 (p0) cc_final: 0.6533 (p0) REVERT: u 29 SER cc_start: 0.9150 (m) cc_final: 0.8890 (t) REVERT: u 115 ASP cc_start: 0.7476 (m-30) cc_final: 0.6965 (m-30) REVERT: u 266 MET cc_start: 0.8457 (mtt) cc_final: 0.8117 (ttm) REVERT: u 283 ARG cc_start: 0.8320 (ttt90) cc_final: 0.7971 (ttt90) REVERT: u 364 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6637 (pm20) REVERT: u 403 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8379 (tt) REVERT: u 412 GLU cc_start: 0.7434 (pm20) cc_final: 0.7161 (pm20) REVERT: u 417 SER cc_start: 0.9023 (m) cc_final: 0.8621 (t) REVERT: u 486 GLU cc_start: 0.7537 (mm-30) cc_final: 0.6978 (tt0) REVERT: u 525 MET cc_start: 0.8813 (tpp) cc_final: 0.8515 (tpp) REVERT: u 550 GLN cc_start: 0.8429 (mt0) cc_final: 0.7915 (mp10) REVERT: u 591 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8036 (tpt170) REVERT: u 594 MET cc_start: 0.8805 (tpp) cc_final: 0.8458 (tpp) REVERT: u 697 ASP cc_start: 0.7520 (p0) cc_final: 0.7188 (p0) REVERT: u 730 THR cc_start: 0.8309 (m) cc_final: 0.7949 (t) REVERT: v 29 SER cc_start: 0.9178 (m) cc_final: 0.8720 (t) REVERT: v 115 ASP cc_start: 0.7694 (m-30) cc_final: 0.7237 (m-30) REVERT: v 308 MET cc_start: 0.8684 (mmm) cc_final: 0.8374 (mmm) REVERT: v 364 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7265 (pm20) REVERT: v 591 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7864 (tpt90) REVERT: v 644 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6338 (tm-30) REVERT: v 742 ARG cc_start: 0.8355 (mmt180) cc_final: 0.8040 (mmp-170) REVERT: w 51 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8842 (pp) REVERT: w 115 ASP cc_start: 0.7791 (m-30) cc_final: 0.7327 (m-30) REVERT: w 272 ASP cc_start: 0.8713 (t0) cc_final: 0.8329 (t70) REVERT: w 308 MET cc_start: 0.8734 (mmm) cc_final: 0.8259 (mmm) REVERT: w 325 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7550 (pp) REVERT: w 364 GLU cc_start: 0.6945 (pm20) cc_final: 0.6718 (pm20) REVERT: w 367 ILE cc_start: 0.9146 (mp) cc_final: 0.8702 (mm) REVERT: w 433 LYS cc_start: 0.9039 (ptpt) cc_final: 0.8790 (ptpt) REVERT: w 478 ASP cc_start: 0.5419 (p0) cc_final: 0.5047 (p0) REVERT: w 674 ASN cc_start: 0.7949 (t0) cc_final: 0.7616 (p0) REVERT: w 701 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.8967 (tp) REVERT: w 731 MET cc_start: 0.8599 (tmm) cc_final: 0.7388 (tmm) REVERT: x 29 SER cc_start: 0.9169 (m) cc_final: 0.8929 (t) REVERT: x 115 ASP cc_start: 0.7708 (m-30) cc_final: 0.7356 (m-30) REVERT: x 325 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.6995 (pp) REVERT: x 364 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7149 (pm20) REVERT: x 387 ASP cc_start: 0.7809 (t0) cc_final: 0.7353 (t0) REVERT: x 533 GLU cc_start: 0.8873 (pm20) cc_final: 0.8670 (pm20) REVERT: x 561 MET cc_start: 0.8483 (tpp) cc_final: 0.7888 (ttt) REVERT: x 591 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7898 (tpt90) REVERT: x 726 ASN cc_start: 0.7836 (m110) cc_final: 0.7469 (m-40) outliers start: 150 outliers final: 99 residues processed: 585 average time/residue: 0.2322 time to fit residues: 220.8679 Evaluate side-chains 545 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 429 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 42 LEU Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 78 TYR Chi-restraints excluded: chain s residue 204 MET Chi-restraints excluded: chain s residue 219 PHE Chi-restraints excluded: chain s residue 290 VAL Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 351 VAL Chi-restraints excluded: chain s residue 364 GLU Chi-restraints excluded: chain s residue 395 VAL Chi-restraints excluded: chain s residue 412 GLU Chi-restraints excluded: chain s residue 445 VAL Chi-restraints excluded: chain s residue 572 PHE Chi-restraints excluded: chain s residue 673 ILE Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain s residue 703 LEU Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 78 TYR Chi-restraints excluded: chain t residue 219 PHE Chi-restraints excluded: chain t residue 223 THR Chi-restraints excluded: chain t residue 253 SER Chi-restraints excluded: chain t residue 344 VAL Chi-restraints excluded: chain t residue 352 PHE Chi-restraints excluded: chain t residue 393 VAL Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 403 LEU Chi-restraints excluded: chain t residue 414 LEU Chi-restraints excluded: chain t residue 457 ASN Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 535 LEU Chi-restraints excluded: chain t residue 667 VAL Chi-restraints excluded: chain t residue 673 ILE Chi-restraints excluded: chain t residue 718 ILE Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 86 ILE Chi-restraints excluded: chain u residue 219 PHE Chi-restraints excluded: chain u residue 223 THR Chi-restraints excluded: chain u residue 247 VAL Chi-restraints excluded: chain u residue 297 TRP Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 395 VAL Chi-restraints excluded: chain u residue 403 LEU Chi-restraints excluded: chain u residue 405 TYR Chi-restraints excluded: chain u residue 414 LEU Chi-restraints excluded: chain u residue 445 VAL Chi-restraints excluded: chain u residue 492 VAL Chi-restraints excluded: chain u residue 591 ARG Chi-restraints excluded: chain u residue 667 VAL Chi-restraints excluded: chain u residue 718 ILE Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 138 THR Chi-restraints excluded: chain v residue 219 PHE Chi-restraints excluded: chain v residue 223 THR Chi-restraints excluded: chain v residue 290 VAL Chi-restraints excluded: chain v residue 305 TRP Chi-restraints excluded: chain v residue 325 LEU Chi-restraints excluded: chain v residue 348 ILE Chi-restraints excluded: chain v residue 364 GLU Chi-restraints excluded: chain v residue 395 VAL Chi-restraints excluded: chain v residue 405 TYR Chi-restraints excluded: chain v residue 430 LEU Chi-restraints excluded: chain v residue 431 THR Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 492 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 542 HIS Chi-restraints excluded: chain v residue 563 VAL Chi-restraints excluded: chain v residue 591 ARG Chi-restraints excluded: chain v residue 673 ILE Chi-restraints excluded: chain v residue 687 THR Chi-restraints excluded: chain v residue 718 ILE Chi-restraints excluded: chain v residue 725 SER Chi-restraints excluded: chain v residue 769 LEU Chi-restraints excluded: chain v residue 792 SER Chi-restraints excluded: chain w residue 51 LEU Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 78 TYR Chi-restraints excluded: chain w residue 121 VAL Chi-restraints excluded: chain w residue 219 PHE Chi-restraints excluded: chain w residue 223 THR Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 403 LEU Chi-restraints excluded: chain w residue 414 LEU Chi-restraints excluded: chain w residue 415 ILE Chi-restraints excluded: chain w residue 423 VAL Chi-restraints excluded: chain w residue 430 LEU Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 585 LEU Chi-restraints excluded: chain w residue 591 ARG Chi-restraints excluded: chain w residue 596 MET Chi-restraints excluded: chain w residue 673 ILE Chi-restraints excluded: chain w residue 687 THR Chi-restraints excluded: chain w residue 701 LEU Chi-restraints excluded: chain w residue 703 LEU Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 219 PHE Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 290 VAL Chi-restraints excluded: chain x residue 304 LEU Chi-restraints excluded: chain x residue 308 MET Chi-restraints excluded: chain x residue 325 LEU Chi-restraints excluded: chain x residue 364 GLU Chi-restraints excluded: chain x residue 395 VAL Chi-restraints excluded: chain x residue 405 TYR Chi-restraints excluded: chain x residue 535 LEU Chi-restraints excluded: chain x residue 572 PHE Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 684 ILE Chi-restraints excluded: chain x residue 718 ILE Chi-restraints excluded: chain x residue 769 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 15 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 276 optimal weight: 0.1980 chunk 314 optimal weight: 0.0980 chunk 467 optimal weight: 2.9990 chunk 205 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 293 optimal weight: 0.5980 chunk 278 optimal weight: 0.9980 chunk 351 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 150 GLN ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 76 GLN ** t 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 207 ASN t 260 ASN ** t 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 190 ASN ** v 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 532 ASN w 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.119046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.090841 restraints weight = 74555.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.093105 restraints weight = 40800.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.094549 restraints weight = 27327.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.095447 restraints weight = 20851.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.095991 restraints weight = 17569.526| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 38748 Z= 0.155 Angle : 0.903 14.733 52692 Z= 0.453 Chirality : 0.052 0.257 5640 Planarity : 0.005 0.062 6918 Dihedral : 7.855 52.114 5216 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 17.35 % Favored : 82.40 % Rotamer: Outliers : 3.52 % Allowed : 20.67 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.78 % 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: -3.84 (0.11), residues: 4716 helix: -2.05 (0.37), residues: 162 sheet: -2.42 (0.13), residues: 1452 loop : -2.79 (0.10), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG u 536 TYR 0.025 0.002 TYR v 77 PHE 0.034 0.002 PHE u 352 TRP 0.040 0.002 TRP v 416 HIS 0.010 0.002 HIS u 67 Details of bonding type rmsd covalent geometry : bond 0.00355 (38748) covalent geometry : angle 0.90252 (52692) hydrogen bonds : bond 0.03331 ( 661) hydrogen bonds : angle 6.93141 ( 1605) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 495 time to evaluate : 1.461 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: s 29 SER cc_start: 0.9108 (m) cc_final: 0.8527 (t) REVERT: s 51 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8281 (pp) REVERT: s 78 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7383 (t80) REVERT: s 115 ASP cc_start: 0.7673 (m-30) cc_final: 0.7181 (m-30) REVERT: s 266 MET cc_start: 0.7885 (ttm) cc_final: 0.7684 (ttm) REVERT: s 283 ARG cc_start: 0.8159 (ttt90) cc_final: 0.7854 (ttt90) REVERT: s 308 MET cc_start: 0.8800 (mmm) cc_final: 0.8371 (mtm) REVERT: s 352 PHE cc_start: 0.8091 (m-80) cc_final: 0.7677 (m-80) REVERT: s 364 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6947 (pm20) REVERT: s 550 GLN cc_start: 0.7957 (mt0) cc_final: 0.7537 (mp10) REVERT: s 666 MET cc_start: 0.7594 (ppp) cc_final: 0.7335 (ppp) REVERT: s 730 THR cc_start: 0.7841 (m) cc_final: 0.7523 (t) REVERT: t 29 SER cc_start: 0.9336 (m) cc_final: 0.9122 (t) REVERT: t 51 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8766 (pp) REVERT: t 78 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.6544 (t80) REVERT: t 92 SER cc_start: 0.8761 (t) cc_final: 0.8409 (m) REVERT: t 115 ASP cc_start: 0.7775 (m-30) cc_final: 0.7336 (m-30) REVERT: t 272 ASP cc_start: 0.8665 (t0) cc_final: 0.8235 (t70) REVERT: t 283 ARG cc_start: 0.8035 (ttt90) cc_final: 0.7787 (ttt90) REVERT: t 308 MET cc_start: 0.8759 (mmm) cc_final: 0.8347 (mmm) REVERT: t 325 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7653 (pp) REVERT: t 367 ILE cc_start: 0.9200 (mp) cc_final: 0.8699 (mm) REVERT: t 430 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7980 (mt) REVERT: t 433 LYS cc_start: 0.8892 (ptpt) cc_final: 0.8610 (ptmt) REVERT: t 457 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8549 (m110) REVERT: t 697 ASP cc_start: 0.7083 (p0) cc_final: 0.6858 (p0) REVERT: t 730 THR cc_start: 0.7777 (m) cc_final: 0.7555 (t) REVERT: u 29 SER cc_start: 0.9188 (m) cc_final: 0.8964 (t) REVERT: u 62 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8375 (tm-30) REVERT: u 115 ASP cc_start: 0.7411 (m-30) cc_final: 0.6923 (m-30) REVERT: u 266 MET cc_start: 0.8365 (mtt) cc_final: 0.7943 (ttm) REVERT: u 272 ASP cc_start: 0.8900 (t0) cc_final: 0.8392 (t0) REVERT: u 283 ARG cc_start: 0.8324 (ttt90) cc_final: 0.7984 (ttt90) REVERT: u 364 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6603 (pm20) REVERT: u 387 ASP cc_start: 0.7774 (t0) cc_final: 0.7372 (t0) REVERT: u 525 MET cc_start: 0.8828 (tpp) cc_final: 0.8535 (tpp) REVERT: u 550 GLN cc_start: 0.8397 (mt0) cc_final: 0.7848 (mp10) REVERT: u 561 MET cc_start: 0.8503 (tpp) cc_final: 0.7983 (ttt) REVERT: u 594 MET cc_start: 0.8742 (tpp) cc_final: 0.8465 (tpp) REVERT: u 697 ASP cc_start: 0.7503 (p0) cc_final: 0.7183 (p0) REVERT: v 29 SER cc_start: 0.9173 (m) cc_final: 0.8666 (t) REVERT: v 115 ASP cc_start: 0.7789 (m-30) cc_final: 0.7326 (m-30) REVERT: v 308 MET cc_start: 0.8758 (mmm) cc_final: 0.8365 (mmm) REVERT: v 364 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7174 (pm20) REVERT: v 567 ASN cc_start: 0.7756 (m-40) cc_final: 0.7543 (m110) REVERT: v 591 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7857 (tpt90) REVERT: v 644 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6139 (tm-30) REVERT: v 742 ARG cc_start: 0.8389 (mmt180) cc_final: 0.8055 (mmm160) REVERT: w 51 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8782 (pp) REVERT: w 115 ASP cc_start: 0.7815 (m-30) cc_final: 0.7282 (m-30) REVERT: w 124 TYR cc_start: 0.8288 (m-80) cc_final: 0.8038 (m-80) REVERT: w 272 ASP cc_start: 0.8788 (t0) cc_final: 0.8368 (t70) REVERT: w 283 ARG cc_start: 0.8187 (ttt90) cc_final: 0.7932 (tpt170) REVERT: w 308 MET cc_start: 0.8798 (mmm) cc_final: 0.8036 (mmm) REVERT: w 325 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7688 (pp) REVERT: w 367 ILE cc_start: 0.9107 (mp) cc_final: 0.8654 (mm) REVERT: w 433 LYS cc_start: 0.9021 (ptpt) cc_final: 0.8736 (ptpt) REVERT: w 645 GLN cc_start: 0.7742 (pp30) cc_final: 0.7501 (pp30) REVERT: w 674 ASN cc_start: 0.7896 (t0) cc_final: 0.7594 (p0) REVERT: w 701 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.8861 (tp) REVERT: w 731 MET cc_start: 0.8641 (tmm) cc_final: 0.7626 (tmm) REVERT: x 29 SER cc_start: 0.9188 (m) cc_final: 0.8984 (t) REVERT: x 115 ASP cc_start: 0.7705 (m-30) cc_final: 0.7369 (m-30) REVERT: x 325 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7130 (pp) REVERT: x 364 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7100 (pm20) REVERT: x 387 ASP cc_start: 0.7863 (t0) cc_final: 0.7439 (t0) REVERT: x 403 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8262 (mp) REVERT: x 533 GLU cc_start: 0.8864 (pm20) cc_final: 0.8650 (pm20) REVERT: x 550 GLN cc_start: 0.8461 (mt0) cc_final: 0.7795 (mp10) REVERT: x 561 MET cc_start: 0.8494 (tpp) cc_final: 0.7914 (ttt) REVERT: x 591 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7762 (tpt90) REVERT: x 726 ASN cc_start: 0.7999 (m110) cc_final: 0.7787 (m-40) outliers start: 145 outliers final: 91 residues processed: 607 average time/residue: 0.2229 time to fit residues: 221.5915 Evaluate side-chains 551 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 441 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 42 LEU Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 78 TYR Chi-restraints excluded: chain s residue 219 PHE Chi-restraints excluded: chain s residue 290 VAL Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 351 VAL Chi-restraints excluded: chain s residue 364 GLU Chi-restraints excluded: chain s residue 395 VAL Chi-restraints excluded: chain s residue 412 GLU Chi-restraints excluded: chain s residue 445 VAL Chi-restraints excluded: chain s residue 673 ILE Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain s residue 703 LEU Chi-restraints excluded: chain s residue 718 ILE Chi-restraints excluded: chain s residue 769 LEU Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 78 TYR Chi-restraints excluded: chain t residue 219 PHE Chi-restraints excluded: chain t residue 223 THR Chi-restraints excluded: chain t residue 325 LEU Chi-restraints excluded: chain t residue 344 VAL Chi-restraints excluded: chain t residue 352 PHE Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 403 LEU Chi-restraints excluded: chain t residue 430 LEU Chi-restraints excluded: chain t residue 457 ASN Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 535 LEU Chi-restraints excluded: chain t residue 667 VAL Chi-restraints excluded: chain t residue 673 ILE Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain u residue 86 ILE Chi-restraints excluded: chain u residue 219 PHE Chi-restraints excluded: chain u residue 223 THR Chi-restraints excluded: chain u residue 247 VAL Chi-restraints excluded: chain u residue 297 TRP Chi-restraints excluded: chain u residue 308 MET Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 395 VAL Chi-restraints excluded: chain u residue 405 TYR Chi-restraints excluded: chain u residue 445 VAL Chi-restraints excluded: chain u residue 492 VAL Chi-restraints excluded: chain u residue 542 HIS Chi-restraints excluded: chain u residue 667 VAL Chi-restraints excluded: chain u residue 718 ILE Chi-restraints excluded: chain v residue 22 LEU Chi-restraints excluded: chain v residue 42 LEU Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 219 PHE Chi-restraints excluded: chain v residue 223 THR Chi-restraints excluded: chain v residue 290 VAL Chi-restraints excluded: chain v residue 325 LEU Chi-restraints excluded: chain v residue 348 ILE Chi-restraints excluded: chain v residue 364 GLU Chi-restraints excluded: chain v residue 395 VAL Chi-restraints excluded: chain v residue 405 TYR Chi-restraints excluded: chain v residue 430 LEU Chi-restraints excluded: chain v residue 431 THR Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 492 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 591 ARG Chi-restraints excluded: chain v residue 673 ILE Chi-restraints excluded: chain v residue 687 THR Chi-restraints excluded: chain v residue 718 ILE Chi-restraints excluded: chain v residue 725 SER Chi-restraints excluded: chain v residue 769 LEU Chi-restraints excluded: chain v residue 792 SER Chi-restraints excluded: chain w residue 51 LEU Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 78 TYR Chi-restraints excluded: chain w residue 121 VAL Chi-restraints excluded: chain w residue 219 PHE Chi-restraints excluded: chain w residue 223 THR Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 403 LEU Chi-restraints excluded: chain w residue 414 LEU Chi-restraints excluded: chain w residue 415 ILE Chi-restraints excluded: chain w residue 430 LEU Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 585 LEU Chi-restraints excluded: chain w residue 591 ARG Chi-restraints excluded: chain w residue 673 ILE Chi-restraints excluded: chain w residue 687 THR Chi-restraints excluded: chain w residue 701 LEU Chi-restraints excluded: chain w residue 718 ILE Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 219 PHE Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 304 LEU Chi-restraints excluded: chain x residue 308 MET Chi-restraints excluded: chain x residue 325 LEU Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 364 GLU Chi-restraints excluded: chain x residue 395 VAL Chi-restraints excluded: chain x residue 403 LEU Chi-restraints excluded: chain x residue 430 LEU Chi-restraints excluded: chain x residue 457 ASN Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 684 ILE Chi-restraints excluded: chain x residue 718 ILE Chi-restraints excluded: chain x residue 769 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 1 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 205 optimal weight: 0.0870 chunk 370 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 391 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 472 optimal weight: 1.9990 chunk 334 optimal weight: 5.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 150 GLN ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 150 GLN ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 477 GLN v 532 ASN ** v 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 477 GLN w 567 ASN ** w 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 457 ASN ** x 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.086895 restraints weight = 76305.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.089848 restraints weight = 40616.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.090730 restraints weight = 23878.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.091215 restraints weight = 18999.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.091330 restraints weight = 18659.050| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 38748 Z= 0.236 Angle : 0.938 16.009 52692 Z= 0.472 Chirality : 0.053 0.243 5640 Planarity : 0.005 0.066 6918 Dihedral : 7.889 52.327 5216 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.30 % Allowed : 18.47 % Favored : 81.23 % Rotamer: Outliers : 3.32 % Allowed : 21.62 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 1.33 % Twisted Proline : 0.93 % Twisted General : 0.71 % 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: -3.85 (0.11), residues: 4716 helix: -1.96 (0.37), residues: 168 sheet: -2.44 (0.13), residues: 1446 loop : -2.79 (0.10), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG t 599 TYR 0.026 0.002 TYR v 77 PHE 0.046 0.002 PHE x 50 TRP 0.052 0.002 TRP v 416 HIS 0.009 0.002 HIS s 249 Details of bonding type rmsd covalent geometry : bond 0.00555 (38748) covalent geometry : angle 0.93846 (52692) hydrogen bonds : bond 0.03428 ( 661) hydrogen bonds : angle 6.97583 ( 1605) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 436 time to evaluate : 1.252 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: s 29 SER cc_start: 0.9176 (m) cc_final: 0.8646 (t) REVERT: s 51 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8427 (pp) REVERT: s 78 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.7390 (t80) REVERT: s 115 ASP cc_start: 0.7895 (m-30) cc_final: 0.7356 (m-30) REVERT: s 266 MET cc_start: 0.7942 (ttm) cc_final: 0.7731 (ttm) REVERT: s 283 ARG cc_start: 0.8243 (ttt90) cc_final: 0.7805 (ttt90) REVERT: s 308 MET cc_start: 0.8928 (mmm) cc_final: 0.8463 (mtm) REVERT: s 364 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7181 (pm20) REVERT: s 367 ILE cc_start: 0.9409 (mm) cc_final: 0.9087 (mm) REVERT: s 550 GLN cc_start: 0.8138 (mt0) cc_final: 0.7812 (mp10) REVERT: s 666 MET cc_start: 0.7738 (ppp) cc_final: 0.7485 (ppp) REVERT: s 730 THR cc_start: 0.8368 (m) cc_final: 0.7970 (t) REVERT: t 29 SER cc_start: 0.9356 (m) cc_final: 0.9140 (t) REVERT: t 51 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8815 (pp) REVERT: t 78 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.6812 (t80) REVERT: t 92 SER cc_start: 0.8841 (t) cc_final: 0.8454 (m) REVERT: t 115 ASP cc_start: 0.7850 (m-30) cc_final: 0.7379 (m-30) REVERT: t 124 TYR cc_start: 0.8538 (m-80) cc_final: 0.8175 (m-80) REVERT: t 272 ASP cc_start: 0.8780 (t0) cc_final: 0.8398 (t70) REVERT: t 308 MET cc_start: 0.8887 (mmm) cc_final: 0.8408 (mmm) REVERT: t 325 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7951 (pp) REVERT: t 430 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8134 (mt) REVERT: t 457 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8632 (m110) REVERT: t 591 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8094 (tpt90) REVERT: t 697 ASP cc_start: 0.7089 (p0) cc_final: 0.6777 (p0) REVERT: u 29 SER cc_start: 0.9240 (m) cc_final: 0.8974 (t) REVERT: u 62 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8297 (tm-30) REVERT: u 115 ASP cc_start: 0.7534 (m-30) cc_final: 0.6966 (m-30) REVERT: u 266 MET cc_start: 0.8474 (mtt) cc_final: 0.8015 (ttm) REVERT: u 283 ARG cc_start: 0.8394 (ttt90) cc_final: 0.8017 (ttt90) REVERT: u 364 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6856 (pm20) REVERT: u 525 MET cc_start: 0.8816 (tpp) cc_final: 0.8568 (tpp) REVERT: u 550 GLN cc_start: 0.8499 (mt0) cc_final: 0.7897 (mp10) REVERT: u 594 MET cc_start: 0.8776 (tpp) cc_final: 0.8411 (tpp) REVERT: u 697 ASP cc_start: 0.7701 (p0) cc_final: 0.7371 (p0) REVERT: u 792 SER cc_start: 0.8944 (OUTLIER) cc_final: 0.8661 (t) REVERT: v 29 SER cc_start: 0.9211 (m) cc_final: 0.8743 (t) REVERT: v 266 MET cc_start: 0.8323 (tpp) cc_final: 0.8030 (tpp) REVERT: v 272 ASP cc_start: 0.9276 (t70) cc_final: 0.8918 (t70) REVERT: v 308 MET cc_start: 0.8862 (mmm) cc_final: 0.8437 (mmm) REVERT: v 364 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7355 (pm20) REVERT: v 591 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7825 (tpt90) REVERT: v 644 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6474 (tm-30) REVERT: v 742 ARG cc_start: 0.8531 (mmt180) cc_final: 0.8009 (mmp-170) REVERT: w 51 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8814 (pp) REVERT: w 115 ASP cc_start: 0.7880 (m-30) cc_final: 0.7324 (m-30) REVERT: w 272 ASP cc_start: 0.8931 (t0) cc_final: 0.8537 (t70) REVERT: w 308 MET cc_start: 0.8933 (mmm) cc_final: 0.8378 (mmm) REVERT: w 325 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7473 (pp) REVERT: w 353 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7268 (m-80) REVERT: w 367 ILE cc_start: 0.9129 (mp) cc_final: 0.8643 (mm) REVERT: w 433 LYS cc_start: 0.9116 (ptpt) cc_final: 0.8833 (ptpt) REVERT: w 477 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7993 (mm-40) REVERT: w 645 GLN cc_start: 0.8045 (pp30) cc_final: 0.7668 (pp30) REVERT: w 701 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9012 (tp) REVERT: w 731 MET cc_start: 0.8718 (tmm) cc_final: 0.7692 (tmm) REVERT: w 789 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8667 (ptm160) REVERT: x 29 SER cc_start: 0.9242 (m) cc_final: 0.9008 (t) REVERT: x 115 ASP cc_start: 0.7811 (m-30) cc_final: 0.7475 (m-30) REVERT: x 272 ASP cc_start: 0.9427 (t0) cc_final: 0.8768 (t0) REVERT: x 283 ARG cc_start: 0.7543 (tpt170) cc_final: 0.7084 (tpm170) REVERT: x 325 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7228 (pp) REVERT: x 364 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7217 (pm20) REVERT: x 387 ASP cc_start: 0.8013 (t0) cc_final: 0.7578 (t0) REVERT: x 403 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8517 (mp) REVERT: x 519 ASP cc_start: 0.6970 (p0) cc_final: 0.6742 (p0) REVERT: x 525 MET cc_start: 0.8979 (tpp) cc_final: 0.8324 (tpp) REVERT: x 533 GLU cc_start: 0.9004 (pm20) cc_final: 0.8733 (pm20) REVERT: x 550 GLN cc_start: 0.8534 (mt0) cc_final: 0.7833 (mp10) REVERT: x 561 MET cc_start: 0.8531 (tpp) cc_final: 0.7984 (ttt) REVERT: x 591 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7778 (tpt90) REVERT: x 594 MET cc_start: 0.8747 (tpp) cc_final: 0.8454 (tpp) REVERT: x 726 ASN cc_start: 0.7956 (m110) cc_final: 0.7640 (m-40) outliers start: 137 outliers final: 91 residues processed: 538 average time/residue: 0.2308 time to fit residues: 202.1856 Evaluate side-chains 533 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 418 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 78 TYR Chi-restraints excluded: chain s residue 219 PHE Chi-restraints excluded: chain s residue 290 VAL Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 351 VAL Chi-restraints excluded: chain s residue 364 GLU Chi-restraints excluded: chain s residue 395 VAL Chi-restraints excluded: chain s residue 412 GLU Chi-restraints excluded: chain s residue 445 VAL Chi-restraints excluded: chain s residue 572 PHE Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain s residue 703 LEU Chi-restraints excluded: chain s residue 718 ILE Chi-restraints excluded: chain s residue 769 LEU Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 78 TYR Chi-restraints excluded: chain t residue 223 THR Chi-restraints excluded: chain t residue 325 LEU Chi-restraints excluded: chain t residue 352 PHE Chi-restraints excluded: chain t residue 393 VAL Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 403 LEU Chi-restraints excluded: chain t residue 430 LEU Chi-restraints excluded: chain t residue 457 ASN Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 535 LEU Chi-restraints excluded: chain t residue 591 ARG Chi-restraints excluded: chain t residue 596 MET Chi-restraints excluded: chain t residue 667 VAL Chi-restraints excluded: chain t residue 673 ILE Chi-restraints excluded: chain t residue 703 LEU Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain u residue 86 ILE Chi-restraints excluded: chain u residue 219 PHE Chi-restraints excluded: chain u residue 223 THR Chi-restraints excluded: chain u residue 247 VAL Chi-restraints excluded: chain u residue 297 TRP Chi-restraints excluded: chain u residue 308 MET Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 395 VAL Chi-restraints excluded: chain u residue 405 TYR Chi-restraints excluded: chain u residue 445 VAL Chi-restraints excluded: chain u residue 492 VAL Chi-restraints excluded: chain u residue 542 HIS Chi-restraints excluded: chain u residue 667 VAL Chi-restraints excluded: chain u residue 718 ILE Chi-restraints excluded: chain u residue 792 SER Chi-restraints excluded: chain v residue 22 LEU Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 204 MET Chi-restraints excluded: chain v residue 223 THR Chi-restraints excluded: chain v residue 290 VAL Chi-restraints excluded: chain v residue 305 TRP Chi-restraints excluded: chain v residue 325 LEU Chi-restraints excluded: chain v residue 348 ILE Chi-restraints excluded: chain v residue 364 GLU Chi-restraints excluded: chain v residue 395 VAL Chi-restraints excluded: chain v residue 405 TYR Chi-restraints excluded: chain v residue 430 LEU Chi-restraints excluded: chain v residue 431 THR Chi-restraints excluded: chain v residue 445 VAL Chi-restraints excluded: chain v residue 492 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 542 HIS Chi-restraints excluded: chain v residue 591 ARG Chi-restraints excluded: chain v residue 687 THR Chi-restraints excluded: chain v residue 718 ILE Chi-restraints excluded: chain v residue 725 SER Chi-restraints excluded: chain v residue 769 LEU Chi-restraints excluded: chain v residue 792 SER Chi-restraints excluded: chain w residue 51 LEU Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 78 TYR Chi-restraints excluded: chain w residue 121 VAL Chi-restraints excluded: chain w residue 219 PHE Chi-restraints excluded: chain w residue 223 THR Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain w residue 353 PHE Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 403 LEU Chi-restraints excluded: chain w residue 413 LEU Chi-restraints excluded: chain w residue 430 LEU Chi-restraints excluded: chain w residue 477 GLN Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 585 LEU Chi-restraints excluded: chain w residue 591 ARG Chi-restraints excluded: chain w residue 673 ILE Chi-restraints excluded: chain w residue 687 THR Chi-restraints excluded: chain w residue 701 LEU Chi-restraints excluded: chain w residue 748 LEU Chi-restraints excluded: chain w residue 789 ARG Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 219 PHE Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 304 LEU Chi-restraints excluded: chain x residue 308 MET Chi-restraints excluded: chain x residue 325 LEU Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 364 GLU Chi-restraints excluded: chain x residue 395 VAL Chi-restraints excluded: chain x residue 403 LEU Chi-restraints excluded: chain x residue 457 ASN Chi-restraints excluded: chain x residue 476 VAL Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 632 THR Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 684 ILE Chi-restraints excluded: chain x residue 718 ILE Chi-restraints excluded: chain x residue 769 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 444 optimal weight: 0.5980 chunk 343 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 389 optimal weight: 3.9990 chunk 255 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 206 optimal weight: 0.7980 chunk 449 optimal weight: 0.8980 chunk 363 optimal weight: 1.9990 chunk 375 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 207 ASN ** s 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 43 GLN ** t 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 74 HIS v 150 GLN ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 477 GLN v 532 ASN w 10 ASN ** w 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 446 GLN w 567 ASN ** x 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 457 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.118690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.090007 restraints weight = 75117.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.092429 restraints weight = 39465.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.093968 restraints weight = 25827.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.094929 restraints weight = 19472.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.095491 restraints weight = 16222.574| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 38748 Z= 0.162 Angle : 0.900 15.975 52692 Z= 0.452 Chirality : 0.052 0.228 5640 Planarity : 0.005 0.061 6918 Dihedral : 7.740 50.101 5216 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 16.69 % Favored : 83.06 % Rotamer: Outliers : 2.98 % Allowed : 22.20 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: -3.71 (0.11), residues: 4716 helix: -1.58 (0.39), residues: 162 sheet: -2.37 (0.13), residues: 1464 loop : -2.68 (0.10), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG x 628 TYR 0.028 0.002 TYR w 124 PHE 0.028 0.002 PHE u 352 TRP 0.057 0.002 TRP v 416 HIS 0.008 0.001 HIS s 249 Details of bonding type rmsd covalent geometry : bond 0.00380 (38748) covalent geometry : angle 0.89998 (52692) hydrogen bonds : bond 0.03333 ( 661) hydrogen bonds : angle 6.95525 ( 1605) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 459 time to evaluate : 1.254 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: s 29 SER cc_start: 0.9217 (m) cc_final: 0.8611 (t) REVERT: s 78 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.7379 (t80) REVERT: s 115 ASP cc_start: 0.7682 (m-30) cc_final: 0.7090 (m-30) REVERT: s 272 ASP cc_start: 0.9149 (t0) cc_final: 0.8927 (t0) REVERT: s 283 ARG cc_start: 0.8090 (ttt90) cc_final: 0.7728 (ttt90) REVERT: s 308 MET cc_start: 0.8818 (mmm) cc_final: 0.8438 (mmm) REVERT: s 314 ARG cc_start: 0.8056 (tpt-90) cc_final: 0.7503 (tpt-90) REVERT: s 352 PHE cc_start: 0.8089 (m-80) cc_final: 0.7754 (m-80) REVERT: s 364 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6823 (pm20) REVERT: s 367 ILE cc_start: 0.9433 (mm) cc_final: 0.9152 (mm) REVERT: s 550 GLN cc_start: 0.8010 (mt0) cc_final: 0.7737 (mp10) REVERT: s 666 MET cc_start: 0.7657 (ppp) cc_final: 0.7358 (ppp) REVERT: s 730 THR cc_start: 0.8141 (m) cc_final: 0.7713 (t) REVERT: t 29 SER cc_start: 0.9380 (m) cc_final: 0.9134 (t) REVERT: t 51 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8791 (pp) REVERT: t 78 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.6767 (t80) REVERT: t 92 SER cc_start: 0.8823 (t) cc_final: 0.8416 (m) REVERT: t 115 ASP cc_start: 0.7795 (m-30) cc_final: 0.7242 (m-30) REVERT: t 118 MET cc_start: 0.9053 (ttt) cc_final: 0.8735 (tmm) REVERT: t 124 TYR cc_start: 0.8422 (m-80) cc_final: 0.8112 (m-80) REVERT: t 272 ASP cc_start: 0.8754 (t0) cc_final: 0.8365 (t70) REVERT: t 308 MET cc_start: 0.8817 (mmm) cc_final: 0.8391 (mmm) REVERT: t 325 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7842 (pp) REVERT: t 367 ILE cc_start: 0.9220 (mp) cc_final: 0.8737 (mm) REVERT: t 430 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8042 (mt) REVERT: t 674 ASN cc_start: 0.8255 (m-40) cc_final: 0.8026 (p0) REVERT: t 718 ILE cc_start: 0.6957 (OUTLIER) cc_final: 0.6689 (mm) REVERT: u 29 SER cc_start: 0.9176 (m) cc_final: 0.8966 (t) REVERT: u 62 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8323 (tm-30) REVERT: u 115 ASP cc_start: 0.7404 (m-30) cc_final: 0.6844 (m-30) REVERT: u 124 TYR cc_start: 0.8422 (m-80) cc_final: 0.8133 (m-80) REVERT: u 266 MET cc_start: 0.8285 (mtt) cc_final: 0.7886 (ttm) REVERT: u 272 ASP cc_start: 0.8821 (t0) cc_final: 0.8506 (t0) REVERT: u 283 ARG cc_start: 0.8281 (ttt90) cc_final: 0.7928 (ttt90) REVERT: u 364 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6784 (pm20) REVERT: u 525 MET cc_start: 0.8816 (tpp) cc_final: 0.8560 (tpp) REVERT: u 550 GLN cc_start: 0.8373 (mt0) cc_final: 0.7736 (mp10) REVERT: u 561 MET cc_start: 0.8510 (tpp) cc_final: 0.7974 (ttt) REVERT: u 594 MET cc_start: 0.8725 (tpp) cc_final: 0.8388 (tpp) REVERT: u 697 ASP cc_start: 0.7669 (p0) cc_final: 0.7406 (p0) REVERT: v 29 SER cc_start: 0.9144 (m) cc_final: 0.8675 (t) REVERT: v 266 MET cc_start: 0.8409 (tpp) cc_final: 0.8205 (tpp) REVERT: v 272 ASP cc_start: 0.9401 (t70) cc_final: 0.9015 (t70) REVERT: v 308 MET cc_start: 0.8757 (mmm) cc_final: 0.8384 (mmm) REVERT: v 364 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: v 591 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8020 (tpt90) REVERT: v 644 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6401 (tm-30) REVERT: v 742 ARG cc_start: 0.8462 (mmt180) cc_final: 0.7990 (mmm160) REVERT: w 51 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8749 (pp) REVERT: w 115 ASP cc_start: 0.7749 (m-30) cc_final: 0.7208 (m-30) REVERT: w 272 ASP cc_start: 0.8838 (t0) cc_final: 0.8449 (t70) REVERT: w 308 MET cc_start: 0.8848 (mmm) cc_final: 0.8039 (mmm) REVERT: w 325 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7725 (pp) REVERT: w 353 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.6846 (m-80) REVERT: w 367 ILE cc_start: 0.9068 (mp) cc_final: 0.8609 (mm) REVERT: w 645 GLN cc_start: 0.7689 (pp30) cc_final: 0.7364 (pp30) REVERT: w 701 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.8928 (tp) REVERT: w 731 MET cc_start: 0.8594 (tmm) cc_final: 0.7450 (tmm) REVERT: x 29 SER cc_start: 0.9267 (m) cc_final: 0.9002 (t) REVERT: x 50 PHE cc_start: 0.7681 (t80) cc_final: 0.7415 (t80) REVERT: x 115 ASP cc_start: 0.7725 (m-30) cc_final: 0.7356 (m-30) REVERT: x 325 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7024 (pp) REVERT: x 364 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7151 (pm20) REVERT: x 403 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8327 (mp) REVERT: x 525 MET cc_start: 0.8921 (tpp) cc_final: 0.8633 (tpp) REVERT: x 533 GLU cc_start: 0.8944 (pm20) cc_final: 0.8719 (pm20) REVERT: x 550 GLN cc_start: 0.8487 (mt0) cc_final: 0.7811 (mp10) REVERT: x 594 MET cc_start: 0.8677 (tpp) cc_final: 0.8461 (tpp) outliers start: 123 outliers final: 84 residues processed: 551 average time/residue: 0.2300 time to fit residues: 206.8921 Evaluate side-chains 533 residues out of total 4122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 431 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 42 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 78 TYR Chi-restraints excluded: chain s residue 124 TYR Chi-restraints excluded: chain s residue 325 LEU Chi-restraints excluded: chain s residue 351 VAL Chi-restraints excluded: chain s residue 364 GLU Chi-restraints excluded: chain s residue 395 VAL Chi-restraints excluded: chain s residue 412 GLU Chi-restraints excluded: chain s residue 445 VAL Chi-restraints excluded: chain s residue 687 THR Chi-restraints excluded: chain s residue 703 LEU Chi-restraints excluded: chain s residue 718 ILE Chi-restraints excluded: chain s residue 769 LEU Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 78 TYR Chi-restraints excluded: chain t residue 223 THR Chi-restraints excluded: chain t residue 325 LEU Chi-restraints excluded: chain t residue 352 PHE Chi-restraints excluded: chain t residue 393 VAL Chi-restraints excluded: chain t residue 395 VAL Chi-restraints excluded: chain t residue 403 LEU Chi-restraints excluded: chain t residue 430 LEU Chi-restraints excluded: chain t residue 514 VAL Chi-restraints excluded: chain t residue 535 LEU Chi-restraints excluded: chain t residue 596 MET Chi-restraints excluded: chain t residue 667 VAL Chi-restraints excluded: chain t residue 673 ILE Chi-restraints excluded: chain t residue 718 ILE Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain u residue 86 ILE Chi-restraints excluded: chain u residue 223 THR Chi-restraints excluded: chain u residue 247 VAL Chi-restraints excluded: chain u residue 292 THR Chi-restraints excluded: chain u residue 297 TRP Chi-restraints excluded: chain u residue 308 MET Chi-restraints excluded: chain u residue 364 GLU Chi-restraints excluded: chain u residue 395 VAL Chi-restraints excluded: chain u residue 405 TYR Chi-restraints excluded: chain u residue 445 VAL Chi-restraints excluded: chain u residue 492 VAL Chi-restraints excluded: chain u residue 542 HIS Chi-restraints excluded: chain u residue 667 VAL Chi-restraints excluded: chain u residue 718 ILE Chi-restraints excluded: chain v residue 22 LEU Chi-restraints excluded: chain v residue 54 LEU Chi-restraints excluded: chain v residue 74 HIS Chi-restraints excluded: chain v residue 124 TYR Chi-restraints excluded: chain v residue 223 THR Chi-restraints excluded: chain v residue 290 VAL Chi-restraints excluded: chain v residue 325 LEU Chi-restraints excluded: chain v residue 348 ILE Chi-restraints excluded: chain v residue 364 GLU Chi-restraints excluded: chain v residue 395 VAL Chi-restraints excluded: chain v residue 405 TYR Chi-restraints excluded: chain v residue 417 SER Chi-restraints excluded: chain v residue 430 LEU Chi-restraints excluded: chain v residue 431 THR Chi-restraints excluded: chain v residue 492 VAL Chi-restraints excluded: chain v residue 514 VAL Chi-restraints excluded: chain v residue 591 ARG Chi-restraints excluded: chain v residue 687 THR Chi-restraints excluded: chain v residue 718 ILE Chi-restraints excluded: chain v residue 725 SER Chi-restraints excluded: chain v residue 769 LEU Chi-restraints excluded: chain v residue 792 SER Chi-restraints excluded: chain w residue 51 LEU Chi-restraints excluded: chain w residue 54 LEU Chi-restraints excluded: chain w residue 78 TYR Chi-restraints excluded: chain w residue 121 VAL Chi-restraints excluded: chain w residue 223 THR Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain w residue 353 PHE Chi-restraints excluded: chain w residue 393 VAL Chi-restraints excluded: chain w residue 395 VAL Chi-restraints excluded: chain w residue 403 LEU Chi-restraints excluded: chain w residue 430 LEU Chi-restraints excluded: chain w residue 477 GLN Chi-restraints excluded: chain w residue 514 VAL Chi-restraints excluded: chain w residue 585 LEU Chi-restraints excluded: chain w residue 591 ARG Chi-restraints excluded: chain w residue 673 ILE Chi-restraints excluded: chain w residue 687 THR Chi-restraints excluded: chain w residue 701 LEU Chi-restraints excluded: chain w residue 748 LEU Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 304 LEU Chi-restraints excluded: chain x residue 308 MET Chi-restraints excluded: chain x residue 325 LEU Chi-restraints excluded: chain x residue 364 GLU Chi-restraints excluded: chain x residue 395 VAL Chi-restraints excluded: chain x residue 403 LEU Chi-restraints excluded: chain x residue 457 ASN Chi-restraints excluded: chain x residue 476 VAL Chi-restraints excluded: chain x residue 632 THR Chi-restraints excluded: chain x residue 673 ILE Chi-restraints excluded: chain x residue 684 ILE Chi-restraints excluded: chain x residue 718 ILE Chi-restraints excluded: chain x residue 769 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 207 optimal weight: 1.9990 chunk 361 optimal weight: 0.6980 chunk 249 optimal weight: 0.7980 chunk 470 optimal weight: 0.0470 chunk 471 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 211 optimal weight: 0.8980 chunk 325 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 327 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 150 GLN ** s 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 74 HIS v 150 GLN ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 477 GLN v 532 ASN v 567 ASN w 10 ASN ** w 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 567 ASN ** x 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.091385 restraints weight = 74964.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.093770 restraints weight = 39936.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.095279 restraints weight = 26327.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.096222 restraints weight = 19902.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.096773 restraints weight = 16635.432| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 38748 Z= 0.163 Angle : 0.895 17.788 52692 Z= 0.448 Chirality : 0.052 0.220 5640 Planarity : 0.005 0.061 6918 Dihedral : 7.602 48.614 5214 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 17.75 % Favored : 82.00 % Rotamer: Outliers : 2.72 % Allowed : 22.51 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: -3.69 (0.11), residues: 4716 helix: -1.51 (0.39), residues: 162 sheet: -2.42 (0.13), residues: 1602 loop : -2.61 (0.11), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG x 628 TYR 0.027 0.002 TYR w 124 PHE 0.027 0.002 PHE s 50 TRP 0.060 0.002 TRP v 416 HIS 0.025 0.002 HIS v 74 Details of bonding type rmsd covalent geometry : bond 0.00386 (38748) covalent geometry : angle 0.89498 (52692) hydrogen bonds : bond 0.03309 ( 661) hydrogen bonds : angle 6.92520 ( 1605) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6902.57 seconds wall clock time: 120 minutes 1.35 seconds (7201.35 seconds total)