Starting phenix.real_space_refine on Wed Aug 5 13:47:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fvd_50803/08_2026/9fvd_50803.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fvd_50803/08_2026/9fvd_50803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fvd_50803/08_2026/9fvd_50803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fvd_50803/08_2026/9fvd_50803.map" model { file = "/net/cci-nas-00/data/ceres_data/9fvd_50803/08_2026/9fvd_50803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fvd_50803/08_2026/9fvd_50803.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 54 5.49 5 S 15 5.16 5 C 6240 2.51 5 N 1833 2.21 5 O 2004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10146 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2991 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 10, 'TRANS': 370} Chain breaks: 2 Chain: "S" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 391 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 11, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "R" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 261 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 9} Chain: "Q" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 130 Classifications: {'RNA': 6} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "U" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 9} Chain: "T" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Restraints were copied for chains: B, C Residues with excluded nonbonded symmetry interactions: 54 residue: pdb=" P A S 1 " occ=0.33 ... (21 atoms not shown) pdb=" OP3 A S 1 " occ=0.33 residue: pdb=" P G S 2 " occ=0.33 ... (21 atoms not shown) pdb=" C4 G S 2 " occ=0.33 residue: pdb=" P A S 3 " occ=0.33 ... (20 atoms not shown) pdb=" C4 A S 3 " occ=0.33 residue: pdb=" P C S 4 " occ=0.33 ... (18 atoms not shown) pdb=" C6 C S 4 " occ=0.33 residue: pdb=" P A S 5 " occ=0.33 ... (20 atoms not shown) pdb=" C4 A S 5 " occ=0.33 residue: pdb=" P C S 6 " occ=0.33 ... (18 atoms not shown) pdb=" C6 C S 6 " occ=0.33 residue: pdb=" P A S 7 " occ=0.33 ... (20 atoms not shown) pdb=" C4 A S 7 " occ=0.33 residue: pdb=" P C S 8 " occ=0.33 ... (18 atoms not shown) pdb=" C6 C S 8 " occ=0.33 residue: pdb=" P A S 9 " occ=0.33 ... (20 atoms not shown) pdb=" C4 A S 9 " occ=0.33 residue: pdb=" P A S 10 " occ=0.33 ... (20 atoms not shown) pdb=" C4 A S 10 " occ=0.33 residue: pdb=" P A S 11 " occ=0.33 ... (20 atoms not shown) pdb=" C4 A S 11 " occ=0.33 residue: pdb=" P A S 12 " occ=0.33 ... (20 atoms not shown) pdb=" C4 A S 12 " occ=0.33 ... (remaining 42 not shown) Time building chain proxies: 2.50, per 1000 atoms: 0.25 Number of scatterers: 10146 At special positions: 0 Unit cell: (86.49, 125.55, 102.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 54 15.00 O 2004 8.00 N 1833 7.00 C 6240 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: 1.27 Conformation dependent library (CDL) restraints added in 315.8 milliseconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 6 sheets defined 76.9% alpha, 4.2% beta 21 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'B' and resid 4 through 13 removed outlier: 4.442A pdb=" N LEU B 10 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLY B 11 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS B 13 " --> pdb=" O LEU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 45 Processing helix chain 'B' and resid 51 through 67 removed outlier: 4.518A pdb=" N GLY B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 99 through 104 removed outlier: 4.292A pdb=" N VAL B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 104' Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 148 through 165 Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 176 through 190 Processing helix chain 'B' and resid 190 through 204 removed outlier: 4.080A pdb=" N LYS B 194 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 249 through 252 removed outlier: 3.673A pdb=" N ARG B 252 " --> pdb=" O PRO B 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 249 through 252' Processing helix chain 'B' and resid 253 through 272 removed outlier: 4.132A pdb=" N GLU B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 287 through 292 removed outlier: 3.659A pdb=" N GLU B 292 " --> pdb=" O ASN B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 311 Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 323 through 350 removed outlier: 3.782A pdb=" N ALA B 350 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 391 removed outlier: 3.509A pdb=" N ARG B 356 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 13 removed outlier: 4.442A pdb=" N LEU A 10 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLY A 11 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 13 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 45 Processing helix chain 'A' and resid 51 through 67 removed outlier: 4.519A pdb=" N GLY A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 76 through 86 Processing helix chain 'A' and resid 99 through 104 removed outlier: 4.292A pdb=" N VAL A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 104' Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 148 through 165 Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 190 through 204 removed outlier: 4.080A pdb=" N LYS A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 249 through 252 removed outlier: 3.673A pdb=" N ARG A 252 " --> pdb=" O PRO A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 252' Processing helix chain 'A' and resid 253 through 272 removed outlier: 4.132A pdb=" N GLU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 287 through 292 removed outlier: 3.659A pdb=" N GLU A 292 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 311 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 323 through 350 removed outlier: 3.782A pdb=" N ALA A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 391 removed outlier: 3.509A pdb=" N ARG A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 13 removed outlier: 4.441A pdb=" N LEU C 10 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLY C 11 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS C 13 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 45 Processing helix chain 'C' and resid 51 through 67 removed outlier: 4.518A pdb=" N GLY C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 99 through 104 removed outlier: 4.292A pdb=" N VAL C 103 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE C 104 " --> pdb=" O PHE C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 104' Processing helix chain 'C' and resid 110 through 118 Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 148 through 165 Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 176 through 190 Processing helix chain 'C' and resid 190 through 204 removed outlier: 4.081A pdb=" N LYS C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 249 through 252 removed outlier: 3.673A pdb=" N ARG C 252 " --> pdb=" O PRO C 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 249 through 252' Processing helix chain 'C' and resid 253 through 272 removed outlier: 4.131A pdb=" N GLU C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 278 No H-bonds generated for 'chain 'C' and resid 276 through 278' Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 287 through 292 removed outlier: 3.659A pdb=" N GLU C 292 " --> pdb=" O ASN C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 311 Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 323 through 350 removed outlier: 3.783A pdb=" N ALA C 350 " --> pdb=" O ILE C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 391 removed outlier: 3.509A pdb=" N ARG C 356 " --> pdb=" O ASP C 352 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 27 Processing sheet with id=AA2, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AA3, first strand: chain 'A' and resid 22 through 27 Processing sheet with id=AA4, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 27 Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 241 609 hydrogen bonds defined for protein. 1719 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3229 1.34 - 1.46: 2166 1.46 - 1.57: 4931 1.57 - 1.69: 103 1.69 - 1.81: 21 Bond restraints: 10450 Sorted by residual: bond pdb=" CG1 ILE A 198 " pdb=" CD1 ILE A 198 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 9.97e-01 bond pdb=" CG1 ILE C 198 " pdb=" CD1 ILE C 198 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.71e-01 bond pdb=" CG1 ILE B 198 " pdb=" CD1 ILE B 198 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.57e-01 bond pdb=" CA ASP C 148 " pdb=" CB ASP C 148 " ideal model delta sigma weight residual 1.534 1.547 -0.013 1.45e-02 4.76e+03 7.76e-01 bond pdb=" CA ASP A 148 " pdb=" CB ASP A 148 " ideal model delta sigma weight residual 1.534 1.546 -0.012 1.45e-02 4.76e+03 7.27e-01 ... (remaining 10445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 13771 1.52 - 3.03: 547 3.03 - 4.55: 65 4.55 - 6.07: 18 6.07 - 7.59: 3 Bond angle restraints: 14404 Sorted by residual: angle pdb=" O5' A R 9 " pdb=" C5' A R 9 " pdb=" C4' A R 9 " ideal model delta sigma weight residual 109.40 111.82 -2.42 8.00e-01 1.56e+00 9.13e+00 angle pdb=" O5' A S 9 " pdb=" C5' A S 9 " pdb=" C4' A S 9 " ideal model delta sigma weight residual 109.40 111.76 -2.36 8.00e-01 1.56e+00 8.70e+00 angle pdb=" O5' A S 3 " pdb=" C5' A S 3 " pdb=" C4' A S 3 " ideal model delta sigma weight residual 109.40 111.75 -2.35 8.00e-01 1.56e+00 8.61e+00 angle pdb=" O5' A U 3 " pdb=" C5' A U 3 " pdb=" C4' A U 3 " ideal model delta sigma weight residual 109.40 111.74 -2.34 8.00e-01 1.56e+00 8.54e+00 angle pdb=" O5' A Q 3 " pdb=" C5' A Q 3 " pdb=" C4' A Q 3 " ideal model delta sigma weight residual 109.40 111.72 -2.32 8.00e-01 1.56e+00 8.42e+00 ... (remaining 14399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5515 17.43 - 34.86: 510 34.86 - 52.29: 101 52.29 - 69.73: 43 69.73 - 87.16: 26 Dihedral angle restraints: 6195 sinusoidal: 2895 harmonic: 3300 Sorted by residual: dihedral pdb=" CA HIS B 208 " pdb=" C HIS B 208 " pdb=" N ASP B 209 " pdb=" CA ASP B 209 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA HIS A 208 " pdb=" C HIS A 208 " pdb=" N ASP A 209 " pdb=" CA ASP A 209 " ideal model delta harmonic sigma weight residual 180.00 163.26 16.74 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA HIS C 208 " pdb=" C HIS C 208 " pdb=" N ASP C 209 " pdb=" CA ASP C 209 " ideal model delta harmonic sigma weight residual 180.00 163.27 16.73 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 6192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1048 0.030 - 0.059: 386 0.059 - 0.089: 178 0.089 - 0.118: 56 0.118 - 0.148: 54 Chirality restraints: 1722 Sorted by residual: chirality pdb=" C2' C U 6 " pdb=" C3' C U 6 " pdb=" O2' C U 6 " pdb=" C1' C U 6 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" C2' C S 6 " pdb=" C3' C S 6 " pdb=" O2' C S 6 " pdb=" C1' C S 6 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" C2' C Q 6 " pdb=" C3' C Q 6 " pdb=" O2' C Q 6 " pdb=" C1' C Q 6 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 1719 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 13 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 14 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 14 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 14 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 13 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO C 14 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 13 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO A 14 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 14 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 14 " 0.027 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 0.01 - 0.99: 1130 0.99 - 1.97: 2634 1.97 - 2.95: 9206 2.95 - 3.92: 36703 3.92 - 4.90: 62521 Warning: very small nonbonded interaction distances. Nonbonded interactions: 112194 Sorted by model distance: nonbonded pdb=" C3' A S 10 " pdb=" C3' A R 16 " model vdw 0.014 3.900 nonbonded pdb=" C3' A S 16 " pdb=" C3' A U 10 " model vdw 0.014 3.900 nonbonded pdb=" C5' G R 17 " pdb=" C5' A U 5 " model vdw 0.014 3.840 nonbonded pdb=" O3' A S 16 " pdb=" O3' A U 10 " model vdw 0.018 3.040 nonbonded pdb=" O3' A S 10 " pdb=" O3' A R 16 " model vdw 0.018 3.040 ... (remaining 112189 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 max=1.00 mean=0.92 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.840 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 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: 23.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10450 Z= 0.162 Angle : 0.658 7.587 14404 Z= 0.375 Chirality : 0.044 0.148 1722 Planarity : 0.005 0.049 1632 Dihedral : 15.199 87.158 4059 Min Nonbonded Distance : 0.014 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.26), residues: 1125 helix: 1.57 (0.19), residues: 741 sheet: -0.91 (0.58), residues: 84 loop : 0.38 (0.43), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 20 TYR 0.025 0.002 TYR A 211 PHE 0.013 0.001 PHE B 195 TRP 0.012 0.002 TRP A 174 HIS 0.004 0.001 HIS C 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (10450) covalent geometry : angle 0.65758 / 0.38 (14404) hydrogen bonds : bond 0.17407 / 11.29 ( 651) hydrogen bonds : angle 5.99784 / 4.27 ( 1719) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 ASP cc_start: 0.8488 (m-30) cc_final: 0.8113 (m-30) REVERT: B 345 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8176 (mm-30) REVERT: A 2 MET cc_start: 0.8445 (ppp) cc_final: 0.8231 (ppp) REVERT: A 28 ASP cc_start: 0.8390 (m-30) cc_final: 0.8101 (m-30) REVERT: A 80 LYS cc_start: 0.8299 (mtmm) cc_final: 0.8061 (mtmm) REVERT: A 212 ASP cc_start: 0.8360 (m-30) cc_final: 0.7947 (m-30) REVERT: A 252 ARG cc_start: 0.8079 (mmt90) cc_final: 0.7833 (mmt90) REVERT: A 257 LYS cc_start: 0.9228 (tppp) cc_final: 0.8923 (mmmm) REVERT: A 323 TYR cc_start: 0.9059 (m-80) cc_final: 0.8726 (m-80) REVERT: A 345 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8098 (mm-30) REVERT: A 380 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8618 (tp40) REVERT: C 80 LYS cc_start: 0.8386 (mtmm) cc_final: 0.7991 (mtmm) REVERT: C 87 TYR cc_start: 0.8547 (m-80) cc_final: 0.8289 (m-80) REVERT: C 180 MET cc_start: 0.8537 (mpp) cc_final: 0.8304 (mpp) REVERT: C 257 LYS cc_start: 0.9206 (tppp) cc_final: 0.8842 (mmmm) REVERT: C 275 GLU cc_start: 0.8213 (mp0) cc_final: 0.7988 (mp0) REVERT: C 292 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7801 (mm-30) REVERT: C 345 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8071 (mm-30) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.1323 time to fit residues: 66.5796 Evaluate side-chains 318 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 HIS ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 HIS A 64 HIS C 18 HIS C 64 HIS C 74 ASN ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 GLN C 380 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.160271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.136911 restraints weight = 20039.343| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.75 r_work: 0.3677 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (19 function evaluations) r_final: 0.3664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.028 0.824 10450 Z= 2.004 Angle : 4.949 85.225 14404 Z= 2.374 Chirality : 0.380 4.364 1722 Planarity : 0.016 0.190 1632 Dihedral : 23.236 150.249 1932 Min Nonbonded Distance : 1.587 Molprobity Statistics. All-atom Clashscore : 55.08 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.11 % Favored : 96.18 % Rotamer: Outliers : 3.36 % Allowed : 16.21 % Favored : 80.43 % Cbeta Deviations : 1.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1125 helix: 1.33 (0.19), residues: 690 sheet: -1.69 (0.88), residues: 30 loop : -0.97 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG A 157 TYR 0.038 0.002 TYR A 211 PHE 0.019 0.002 PHE C 195 TRP 0.007 0.001 TRP A 174 HIS 0.033 0.002 HIS C 293 Details of bonding type rmsd/Z covalent geometry : bond 0.02757 / 2.00 (10450) covalent geometry : angle 4.94861 / 2.37 (14404) hydrogen bonds : bond 0.63914 / 39.50 ( 651) hydrogen bonds : angle 5.84065 / 4.17 ( 1719) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 334 time to evaluate : 0.379 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: B 65 TYR cc_start: 0.6649 (m-80) cc_final: 0.6294 (m-80) REVERT: B 80 LYS cc_start: 0.8365 (mtmm) cc_final: 0.8087 (mtmm) REVERT: B 81 TYR cc_start: 0.8551 (t80) cc_final: 0.8301 (t80) REVERT: B 180 MET cc_start: 0.8790 (mpp) cc_final: 0.8430 (mpp) REVERT: B 198 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9013 (mp) REVERT: B 212 ASP cc_start: 0.8976 (m-30) cc_final: 0.8652 (m-30) REVERT: B 325 GLN cc_start: 0.8601 (mp10) cc_final: 0.8379 (mp10) REVERT: B 340 ARG cc_start: 0.8510 (tpt90) cc_final: 0.8164 (mmm160) REVERT: B 345 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8276 (mm-30) REVERT: B 380 GLN cc_start: 0.9002 (tp40) cc_final: 0.8757 (tp40) REVERT: A 47 ILE cc_start: 0.9225 (mm) cc_final: 0.8901 (mp) REVERT: A 188 ARG cc_start: 0.8392 (tpt90) cc_final: 0.8149 (tpt-90) REVERT: A 198 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8942 (mp) REVERT: A 212 ASP cc_start: 0.8874 (m-30) cc_final: 0.8579 (m-30) REVERT: A 345 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8313 (mm-30) REVERT: A 383 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8336 (tm-30) REVERT: C 32 GLN cc_start: 0.8783 (tp-100) cc_final: 0.8548 (tp-100) REVERT: C 65 TYR cc_start: 0.6959 (m-10) cc_final: 0.6685 (m-80) REVERT: C 80 LYS cc_start: 0.8516 (mtmm) cc_final: 0.8128 (mtmm) REVERT: C 164 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8000 (tt0) REVERT: C 180 MET cc_start: 0.8836 (mpp) cc_final: 0.8464 (mpp) REVERT: C 198 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9065 (mp) REVERT: C 275 GLU cc_start: 0.8983 (mp0) cc_final: 0.8774 (mp0) REVERT: C 325 GLN cc_start: 0.8865 (mp10) cc_final: 0.8627 (mp10) REVERT: C 345 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8365 (mm-30) REVERT: C 356 ARG cc_start: 0.7785 (mmt-90) cc_final: 0.7286 (mmt-90) REVERT: C 357 LYS cc_start: 0.9054 (mtmm) cc_final: 0.8821 (mtmm) outliers start: 33 outliers final: 13 residues processed: 356 average time/residue: 0.1286 time to fit residues: 60.6582 Evaluate side-chains 332 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 316 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 380 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 78 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 49 optimal weight: 0.0000 chunk 108 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN A 284 ASN A 380 GLN C 37 ASN ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.163920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.139893 restraints weight = 19826.532| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 3.85 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3885 r_free = 0.3885 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.3880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.7718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.477 10450 Z= 1.092 Angle : 3.095 76.672 14404 Z= 1.552 Chirality : 0.331 4.515 1722 Planarity : 0.011 0.135 1632 Dihedral : 22.322 156.255 1932 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 57.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.20 % Allowed : 16.72 % Favored : 78.08 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.25), residues: 1125 helix: 0.89 (0.19), residues: 726 sheet: -1.89 (0.88), residues: 30 loop : -1.33 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 281 TYR 0.042 0.004 TYR C 323 PHE 0.022 0.002 PHE B 224 TRP 0.005 0.001 TRP A 174 HIS 0.016 0.002 HIS C 293 Details of bonding type rmsd/Z covalent geometry : bond 0.01545 / 1.09 (10450) covalent geometry : angle 3.09533 / 1.55 (14404) hydrogen bonds : bond 0.72061 / 46.92 ( 651) hydrogen bonds : angle 5.63001 / 4.02 ( 1719) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 365 time to evaluate : 0.352 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: B 65 TYR cc_start: 0.6448 (m-80) cc_final: 0.6191 (m-80) REVERT: B 88 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8049 (mm-30) REVERT: B 133 PHE cc_start: 0.8580 (t80) cc_final: 0.8352 (t80) REVERT: B 180 MET cc_start: 0.8710 (mpp) cc_final: 0.8466 (mpp) REVERT: B 198 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9048 (mp) REVERT: B 212 ASP cc_start: 0.8589 (m-30) cc_final: 0.8215 (m-30) REVERT: B 252 ARG cc_start: 0.8107 (mmt90) cc_final: 0.7865 (mmt90) REVERT: B 308 THR cc_start: 0.8081 (m) cc_final: 0.7773 (m) REVERT: B 319 VAL cc_start: 0.2838 (OUTLIER) cc_final: 0.2530 (t) REVERT: B 345 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8246 (mm-30) REVERT: B 356 ARG cc_start: 0.7660 (mmt-90) cc_final: 0.7343 (mmt-90) REVERT: B 383 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8101 (tm-30) REVERT: A 65 TYR cc_start: 0.5595 (m-80) cc_final: 0.5304 (m-80) REVERT: A 80 LYS cc_start: 0.8498 (mtmm) cc_final: 0.8037 (mtmm) REVERT: A 84 ASP cc_start: 0.7965 (m-30) cc_final: 0.7745 (m-30) REVERT: A 148 ASP cc_start: 0.6982 (p0) cc_final: 0.6554 (p0) REVERT: A 149 ARG cc_start: 0.7701 (mmm160) cc_final: 0.7291 (mmm160) REVERT: A 152 ILE cc_start: 0.9093 (pt) cc_final: 0.8849 (pt) REVERT: A 163 GLN cc_start: 0.7549 (mt0) cc_final: 0.7042 (mt0) REVERT: A 173 HIS cc_start: 0.7740 (t70) cc_final: 0.7529 (t70) REVERT: A 198 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.9053 (mp) REVERT: A 252 ARG cc_start: 0.8257 (mmt90) cc_final: 0.8034 (mmt90) REVERT: A 259 GLU cc_start: 0.8633 (mm-30) cc_final: 0.7833 (mm-30) REVERT: A 288 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8017 (tp) REVERT: A 295 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8158 (mp) REVERT: A 308 THR cc_start: 0.7828 (m) cc_final: 0.7253 (m) REVERT: A 342 GLU cc_start: 0.8245 (pp20) cc_final: 0.7780 (pp20) REVERT: A 345 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8204 (mm-30) REVERT: A 356 ARG cc_start: 0.7568 (mmt-90) cc_final: 0.7130 (mmt-90) REVERT: A 383 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8320 (tm-30) REVERT: C 32 GLN cc_start: 0.8779 (tp-100) cc_final: 0.8526 (tp-100) REVERT: C 81 TYR cc_start: 0.8563 (t80) cc_final: 0.8266 (t80) REVERT: C 180 MET cc_start: 0.8655 (mpp) cc_final: 0.8437 (mpp) REVERT: C 198 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9090 (mp) REVERT: C 234 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9124 (mm) REVERT: C 252 ARG cc_start: 0.8241 (mmt90) cc_final: 0.7932 (mmt90) REVERT: C 288 ILE cc_start: 0.8785 (tp) cc_final: 0.8396 (tp) REVERT: C 325 GLN cc_start: 0.8732 (mp10) cc_final: 0.8345 (mp10) REVERT: C 343 HIS cc_start: 0.8235 (t-90) cc_final: 0.7918 (t-90) REVERT: C 345 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8225 (mm-30) REVERT: C 352 ASP cc_start: 0.8415 (p0) cc_final: 0.7956 (p0) REVERT: C 356 ARG cc_start: 0.7520 (mmt-90) cc_final: 0.6632 (mpt180) outliers start: 51 outliers final: 17 residues processed: 392 average time/residue: 0.1237 time to fit residues: 64.5944 Evaluate side-chains 365 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 341 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 234 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 113 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 51 optimal weight: 0.0980 chunk 110 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 HIS B 380 GLN A 284 ASN C 37 ASN ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.167108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.142281 restraints weight = 19687.650| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 3.89 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3923 r_free = 0.3923 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3923 r_free = 0.3923 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.8483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.182 10450 Z= 0.763 Angle : 2.458 51.954 14404 Z= 1.262 Chirality : 0.322 4.525 1722 Planarity : 0.010 0.233 1632 Dihedral : 21.973 173.545 1932 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 52.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.81 % Allowed : 19.88 % Favored : 74.31 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.25), residues: 1125 helix: 0.77 (0.19), residues: 726 sheet: -2.24 (0.87), residues: 30 loop : -1.31 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.002 ARG C 188 TYR 0.035 0.003 TYR C 65 PHE 0.021 0.002 PHE C 184 TRP 0.005 0.001 TRP A 174 HIS 0.013 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.01102 / 0.76 (10450) covalent geometry : angle 2.45752 / 1.26 (14404) hydrogen bonds : bond 0.69684 / 45.82 ( 651) hydrogen bonds : angle 5.53436 / 3.97 ( 1719) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 377 time to evaluate : 0.368 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: B 80 LYS cc_start: 0.8471 (mtmm) cc_final: 0.8170 (mtmm) REVERT: B 88 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7903 (mm-30) REVERT: B 194 LYS cc_start: 0.8931 (mttm) cc_final: 0.8441 (mttm) REVERT: B 198 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9022 (mp) REVERT: B 252 ARG cc_start: 0.8070 (mmt90) cc_final: 0.7725 (mmt90) REVERT: B 259 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8289 (mm-30) REVERT: B 308 THR cc_start: 0.7991 (m) cc_final: 0.7548 (m) REVERT: B 336 LYS cc_start: 0.9170 (mptt) cc_final: 0.8943 (mmtp) REVERT: B 345 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8291 (mm-30) REVERT: B 356 ARG cc_start: 0.7598 (mmt-90) cc_final: 0.7327 (mmt-90) REVERT: B 383 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8186 (tm-30) REVERT: A 80 LYS cc_start: 0.8425 (mtmm) cc_final: 0.7964 (mtmm) REVERT: A 84 ASP cc_start: 0.7946 (m-30) cc_final: 0.7665 (m-30) REVERT: A 149 ARG cc_start: 0.7286 (mmm160) cc_final: 0.6725 (mmm160) REVERT: A 152 ILE cc_start: 0.9067 (pt) cc_final: 0.8817 (pt) REVERT: A 153 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7441 (mm-30) REVERT: A 198 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.9077 (mp) REVERT: A 252 ARG cc_start: 0.8256 (mmt90) cc_final: 0.8008 (mmt90) REVERT: A 288 ILE cc_start: 0.8265 (tp) cc_final: 0.7912 (tp) REVERT: A 308 THR cc_start: 0.7968 (m) cc_final: 0.7393 (m) REVERT: A 345 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8230 (mm-30) REVERT: A 356 ARG cc_start: 0.7571 (mmt-90) cc_final: 0.7163 (mmt-90) REVERT: A 357 LYS cc_start: 0.8857 (mtmt) cc_final: 0.8522 (mtmm) REVERT: A 383 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8191 (tm-30) REVERT: A 387 ARG cc_start: 0.8626 (ptp90) cc_final: 0.8257 (ptp90) REVERT: C 23 LYS cc_start: 0.7976 (mmpt) cc_final: 0.7738 (mmpt) REVERT: C 27 PHE cc_start: 0.8572 (m-10) cc_final: 0.8301 (m-10) REVERT: C 32 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8547 (tp-100) REVERT: C 64 HIS cc_start: 0.8799 (t-90) cc_final: 0.8551 (t-90) REVERT: C 80 LYS cc_start: 0.8495 (mtmm) cc_final: 0.8150 (mtmm) REVERT: C 198 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9092 (mp) REVERT: C 223 ARG cc_start: 0.8454 (mtp85) cc_final: 0.8238 (ttt90) REVERT: C 234 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8996 (mm) REVERT: C 252 ARG cc_start: 0.8267 (mmt90) cc_final: 0.7889 (mmt90) REVERT: C 255 LYS cc_start: 0.3920 (mmtt) cc_final: 0.3461 (mmtt) REVERT: C 257 LYS cc_start: 0.9170 (tppp) cc_final: 0.8871 (mmmm) REVERT: C 308 THR cc_start: 0.7794 (m) cc_final: 0.7479 (m) REVERT: C 345 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8256 (mm-30) REVERT: C 356 ARG cc_start: 0.7482 (mmt-90) cc_final: 0.6843 (mmt-90) REVERT: C 383 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8153 (tm-30) outliers start: 57 outliers final: 29 residues processed: 407 average time/residue: 0.1220 time to fit residues: 65.9137 Evaluate side-chains 392 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 359 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 382 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 71 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 21 ASN C 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.168815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.143170 restraints weight = 19593.867| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 3.93 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3951 r_free = 0.3951 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3951 r_free = 0.3951 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.9026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.187 10450 Z= 0.627 Angle : 2.178 63.340 14404 Z= 1.114 Chirality : 0.293 4.569 1722 Planarity : 0.009 0.188 1632 Dihedral : 21.651 174.108 1932 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 49.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.40 % Allowed : 21.81 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1125 helix: 0.69 (0.19), residues: 711 sheet: -2.32 (0.89), residues: 30 loop : -1.26 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.001 ARG C 327 TYR 0.046 0.004 TYR B 65 PHE 0.029 0.002 PHE C 184 TRP 0.007 0.001 TRP A 174 HIS 0.006 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00943 / 0.63 (10450) covalent geometry : angle 2.17831 / 1.11 (14404) hydrogen bonds : bond 0.64524 / 42.76 ( 651) hydrogen bonds : angle 5.40063 / 3.87 ( 1719) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 381 time to evaluate : 0.228 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: B 65 TYR cc_start: 0.6027 (m-80) cc_final: 0.5659 (m-80) REVERT: B 88 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7900 (tp30) REVERT: B 133 PHE cc_start: 0.8453 (t80) cc_final: 0.8157 (t80) REVERT: B 194 LYS cc_start: 0.8996 (mttm) cc_final: 0.8413 (mttm) REVERT: B 198 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9091 (mp) REVERT: B 252 ARG cc_start: 0.8104 (mmt90) cc_final: 0.7685 (mmt90) REVERT: B 259 GLU cc_start: 0.8523 (mm-30) cc_final: 0.7970 (mm-30) REVERT: B 308 THR cc_start: 0.8090 (m) cc_final: 0.7634 (m) REVERT: B 327 ARG cc_start: 0.8088 (ttp-110) cc_final: 0.7661 (ttp-110) REVERT: B 336 LYS cc_start: 0.9167 (mptt) cc_final: 0.8950 (mmtp) REVERT: B 345 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8349 (mm-30) REVERT: B 356 ARG cc_start: 0.7676 (mmt-90) cc_final: 0.7248 (mmt-90) REVERT: B 383 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8201 (tm-30) REVERT: A 3 ASP cc_start: 0.9062 (t0) cc_final: 0.8758 (t0) REVERT: A 44 ASN cc_start: 0.9178 (p0) cc_final: 0.8789 (p0) REVERT: A 64 HIS cc_start: 0.8663 (t-90) cc_final: 0.8413 (t-90) REVERT: A 80 LYS cc_start: 0.8420 (mtmm) cc_final: 0.7921 (mtmm) REVERT: A 84 ASP cc_start: 0.7982 (m-30) cc_final: 0.7693 (m-30) REVERT: A 149 ARG cc_start: 0.7109 (mmm160) cc_final: 0.6604 (mmm160) REVERT: A 152 ILE cc_start: 0.9013 (pt) cc_final: 0.8744 (pt) REVERT: A 153 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7474 (mm-30) REVERT: A 180 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8456 (mpp) REVERT: A 198 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9083 (mp) REVERT: A 252 ARG cc_start: 0.8296 (mmt90) cc_final: 0.7999 (mmt90) REVERT: A 288 ILE cc_start: 0.8305 (tp) cc_final: 0.8010 (tp) REVERT: A 331 HIS cc_start: 0.7275 (t70) cc_final: 0.7060 (t70) REVERT: A 345 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8268 (mm-30) REVERT: A 354 GLU cc_start: 0.8733 (tp30) cc_final: 0.8384 (pt0) REVERT: A 356 ARG cc_start: 0.7743 (mmt-90) cc_final: 0.7321 (mmt-90) REVERT: A 383 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8073 (tm-30) REVERT: A 387 ARG cc_start: 0.8587 (ptp90) cc_final: 0.8175 (ptp90) REVERT: C 32 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8465 (tp-100) REVERT: C 80 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8023 (mtmm) REVERT: C 180 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8491 (mpp) REVERT: C 198 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9041 (mp) REVERT: C 234 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8998 (mm) REVERT: C 252 ARG cc_start: 0.8282 (mmt90) cc_final: 0.7869 (mmt90) REVERT: C 255 LYS cc_start: 0.3291 (mmtt) cc_final: 0.2673 (mmtt) REVERT: C 257 LYS cc_start: 0.9119 (tppp) cc_final: 0.8753 (mmmm) REVERT: C 308 THR cc_start: 0.7611 (m) cc_final: 0.7108 (m) REVERT: C 328 GLU cc_start: 0.8233 (mm-30) cc_final: 0.8019 (mm-30) REVERT: C 345 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8255 (mm-30) REVERT: C 354 GLU cc_start: 0.8915 (tp30) cc_final: 0.7985 (tp30) REVERT: C 356 ARG cc_start: 0.7581 (mmt-90) cc_final: 0.6888 (mmt-90) REVERT: C 357 LYS cc_start: 0.8793 (mtmm) cc_final: 0.8297 (mtmm) outliers start: 53 outliers final: 32 residues processed: 405 average time/residue: 0.1227 time to fit residues: 65.9711 Evaluate side-chains 390 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 352 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 374 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 54 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 371 HIS A 32 GLN A 380 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.172150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.145841 restraints weight = 19845.055| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 4.03 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3974 r_free = 0.3974 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3975 r_free = 0.3975 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (13 function evaluations) r_final: 0.3975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.9583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.193 10450 Z= 0.552 Angle : 2.028 47.048 14404 Z= 1.024 Chirality : 0.272 4.783 1722 Planarity : 0.008 0.138 1632 Dihedral : 21.990 177.130 1932 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 46.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.61 % Allowed : 22.43 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.25), residues: 1125 helix: 0.47 (0.19), residues: 732 sheet: -1.32 (0.62), residues: 78 loop : -1.12 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 327 TYR 0.032 0.003 TYR A 65 PHE 0.070 0.003 PHE C 184 TRP 0.009 0.001 TRP A 174 HIS 0.012 0.001 HIS C 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00833 / 0.55 (10450) covalent geometry : angle 2.02760 / 1.02 (14404) hydrogen bonds : bond 0.59958 / 39.53 ( 651) hydrogen bonds : angle 5.38170 / 3.84 ( 1719) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 380 time to evaluate : 0.340 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: B 80 LYS cc_start: 0.8549 (mtmm) cc_final: 0.8171 (mtmm) REVERT: B 133 PHE cc_start: 0.8537 (t80) cc_final: 0.8280 (t80) REVERT: B 194 LYS cc_start: 0.9026 (mttm) cc_final: 0.8632 (mttm) REVERT: B 198 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9095 (mp) REVERT: B 308 THR cc_start: 0.7939 (m) cc_final: 0.7551 (m) REVERT: B 336 LYS cc_start: 0.9189 (mptt) cc_final: 0.8946 (mmtp) REVERT: B 345 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8409 (mm-30) REVERT: B 356 ARG cc_start: 0.7624 (mmt-90) cc_final: 0.7115 (mmt-90) REVERT: B 365 GLN cc_start: 0.8817 (tp40) cc_final: 0.8452 (tp-100) REVERT: B 383 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8172 (tm-30) REVERT: A 3 ASP cc_start: 0.9058 (t0) cc_final: 0.8722 (t0) REVERT: A 44 ASN cc_start: 0.9196 (p0) cc_final: 0.8829 (p0) REVERT: A 80 LYS cc_start: 0.8449 (mtmm) cc_final: 0.7996 (mtmm) REVERT: A 81 TYR cc_start: 0.8550 (t80) cc_final: 0.8312 (t80) REVERT: A 84 ASP cc_start: 0.7992 (m-30) cc_final: 0.7707 (m-30) REVERT: A 153 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7697 (mm-30) REVERT: A 180 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8381 (mpp) REVERT: A 194 LYS cc_start: 0.8914 (mttm) cc_final: 0.8596 (mttt) REVERT: A 198 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9083 (mp) REVERT: A 288 ILE cc_start: 0.8393 (tp) cc_final: 0.8142 (tp) REVERT: A 308 THR cc_start: 0.7836 (m) cc_final: 0.7188 (m) REVERT: A 345 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8273 (mm-30) REVERT: A 356 ARG cc_start: 0.7771 (mmt-90) cc_final: 0.7202 (mmt-90) REVERT: A 383 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8379 (tm-30) REVERT: C 3 ASP cc_start: 0.8801 (t0) cc_final: 0.8557 (t0) REVERT: C 32 GLN cc_start: 0.8692 (tp-100) cc_final: 0.8376 (tp-100) REVERT: C 80 LYS cc_start: 0.8520 (mtmm) cc_final: 0.8088 (mtmm) REVERT: C 153 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8423 (tm-30) REVERT: C 180 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8438 (mpp) REVERT: C 194 LYS cc_start: 0.8723 (mttm) cc_final: 0.8315 (mttm) REVERT: C 198 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9104 (mp) REVERT: C 234 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8931 (mm) REVERT: C 250 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8635 (tt) REVERT: C 252 ARG cc_start: 0.8299 (mmt90) cc_final: 0.7916 (mmt90) REVERT: C 255 LYS cc_start: 0.2934 (mmtt) cc_final: 0.2219 (mmtt) REVERT: C 308 THR cc_start: 0.7712 (OUTLIER) cc_final: 0.6897 (m) REVERT: C 345 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8314 (mm-30) REVERT: C 354 GLU cc_start: 0.8951 (tp30) cc_final: 0.8095 (tp30) REVERT: C 356 ARG cc_start: 0.7551 (mmt-90) cc_final: 0.6814 (mmt-90) REVERT: C 357 LYS cc_start: 0.8771 (mtmm) cc_final: 0.8329 (mtmm) outliers start: 55 outliers final: 29 residues processed: 407 average time/residue: 0.1293 time to fit residues: 69.4491 Evaluate side-chains 382 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 345 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 385 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 23 optimal weight: 0.4980 chunk 61 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.172349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.146414 restraints weight = 19402.652| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 3.89 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3982 r_free = 0.3982 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3984 r_free = 0.3984 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.9982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.163 10450 Z= 0.516 Angle : 1.929 47.560 14404 Z= 0.986 Chirality : 0.261 4.589 1722 Planarity : 0.009 0.107 1632 Dihedral : 21.944 176.060 1932 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 50.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.99 % Allowed : 25.18 % Favored : 69.83 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.25), residues: 1125 helix: 0.76 (0.19), residues: 693 sheet: -2.47 (0.84), residues: 30 loop : -1.35 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 188 TYR 0.042 0.004 TYR B 65 PHE 0.054 0.003 PHE C 184 TRP 0.009 0.001 TRP A 174 HIS 0.010 0.001 HIS C 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00799 / 0.52 (10450) covalent geometry : angle 1.92904 / 0.99 (14404) hydrogen bonds : bond 0.56549 / 37.85 ( 651) hydrogen bonds : angle 5.40009 / 3.84 ( 1719) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 361 time to evaluate : 0.359 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: B 80 LYS cc_start: 0.8458 (mtmm) cc_final: 0.8088 (mtmm) REVERT: B 133 PHE cc_start: 0.8604 (t80) cc_final: 0.8380 (t80) REVERT: B 194 LYS cc_start: 0.8978 (mttm) cc_final: 0.8573 (mttm) REVERT: B 198 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9109 (mp) REVERT: B 259 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8119 (mm-30) REVERT: B 336 LYS cc_start: 0.9227 (mptt) cc_final: 0.8952 (mmtp) REVERT: B 345 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8463 (mm-30) REVERT: B 365 GLN cc_start: 0.8774 (tp40) cc_final: 0.8433 (tp-100) REVERT: B 382 ARG cc_start: 0.8573 (mmp80) cc_final: 0.8228 (mmp-170) REVERT: B 383 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8168 (tm-30) REVERT: A 3 ASP cc_start: 0.9017 (t0) cc_final: 0.8713 (t0) REVERT: A 44 ASN cc_start: 0.9221 (p0) cc_final: 0.8813 (p0) REVERT: A 47 ILE cc_start: 0.9136 (mm) cc_final: 0.8874 (mp) REVERT: A 80 LYS cc_start: 0.8432 (mtmm) cc_final: 0.7968 (mtmm) REVERT: A 81 TYR cc_start: 0.8574 (t80) cc_final: 0.8336 (t80) REVERT: A 84 ASP cc_start: 0.7998 (m-30) cc_final: 0.7706 (m-30) REVERT: A 180 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8462 (mpp) REVERT: A 194 LYS cc_start: 0.8955 (mttm) cc_final: 0.8724 (mtmm) REVERT: A 198 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9088 (mp) REVERT: A 209 ASP cc_start: 0.8062 (p0) cc_final: 0.7855 (p0) REVERT: A 252 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.7564 (mmt90) REVERT: A 257 LYS cc_start: 0.8960 (tppp) cc_final: 0.8411 (tppp) REVERT: A 288 ILE cc_start: 0.8447 (tp) cc_final: 0.8178 (tp) REVERT: A 319 VAL cc_start: 0.0557 (OUTLIER) cc_final: 0.0042 (t) REVERT: A 345 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8287 (mm-30) REVERT: A 356 ARG cc_start: 0.7621 (mmt-90) cc_final: 0.7021 (mmt-90) REVERT: A 365 GLN cc_start: 0.8944 (tp40) cc_final: 0.8515 (tp-100) REVERT: A 383 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8372 (tm-30) REVERT: C 3 ASP cc_start: 0.8716 (t0) cc_final: 0.8430 (t0) REVERT: C 32 GLN cc_start: 0.8673 (tp-100) cc_final: 0.8345 (tp-100) REVERT: C 80 LYS cc_start: 0.8496 (mtmm) cc_final: 0.8056 (mtmm) REVERT: C 165 GLN cc_start: 0.3531 (OUTLIER) cc_final: 0.3331 (mt0) REVERT: C 180 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8590 (mpp) REVERT: C 194 LYS cc_start: 0.8679 (mttm) cc_final: 0.8244 (mttm) REVERT: C 198 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9120 (mp) REVERT: C 211 TYR cc_start: 0.7172 (m-80) cc_final: 0.6950 (m-10) REVERT: C 234 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9002 (mm) REVERT: C 250 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8657 (tt) REVERT: C 252 ARG cc_start: 0.8373 (mmt90) cc_final: 0.8095 (mmt90) REVERT: C 255 LYS cc_start: 0.2591 (mmtt) cc_final: 0.1715 (mmtt) REVERT: C 308 THR cc_start: 0.7125 (OUTLIER) cc_final: 0.6362 (m) REVERT: C 328 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8183 (mm-30) REVERT: C 345 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8300 (mm-30) REVERT: C 356 ARG cc_start: 0.7574 (mmt-90) cc_final: 0.7087 (mmt-90) REVERT: C 357 LYS cc_start: 0.8776 (mtmm) cc_final: 0.8331 (mtmm) REVERT: C 383 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8137 (tm-30) outliers start: 49 outliers final: 30 residues processed: 383 average time/residue: 0.1289 time to fit residues: 65.5773 Evaluate side-chains 377 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 337 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 385 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 66 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 33 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 371 HIS C 37 ASN ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.175821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.149978 restraints weight = 19077.896| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 3.77 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (13 function evaluations) r_final: 0.4028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 1.0401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.151 10450 Z= 0.497 Angle : 1.882 46.408 14404 Z= 0.960 Chirality : 0.240 4.540 1722 Planarity : 0.008 0.123 1632 Dihedral : 22.005 177.865 1932 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 48.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.89 % Allowed : 25.99 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.26), residues: 1125 helix: 0.47 (0.19), residues: 726 sheet: -1.68 (0.56), residues: 72 loop : -1.12 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 188 TYR 0.030 0.003 TYR A 65 PHE 0.078 0.003 PHE C 184 TRP 0.008 0.001 TRP A 174 HIS 0.010 0.001 HIS C 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00772 / 0.50 (10450) covalent geometry : angle 1.88167 / 0.96 (14404) hydrogen bonds : bond 0.55190 / 36.76 ( 651) hydrogen bonds : angle 5.45510 / 3.91 ( 1719) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 364 time to evaluate : 0.370 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: B 80 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8203 (mtmm) REVERT: B 133 PHE cc_start: 0.8664 (t80) cc_final: 0.8452 (t80) REVERT: B 194 LYS cc_start: 0.8963 (mttm) cc_final: 0.8285 (mttm) REVERT: B 228 LEU cc_start: 0.7482 (mt) cc_final: 0.7248 (mp) REVERT: B 257 LYS cc_start: 0.8929 (tppp) cc_final: 0.8696 (mmtp) REVERT: B 259 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7224 (mm-30) REVERT: B 308 THR cc_start: 0.7364 (m) cc_final: 0.7105 (m) REVERT: B 336 LYS cc_start: 0.9207 (mptt) cc_final: 0.8968 (mmtp) REVERT: B 365 GLN cc_start: 0.8742 (tp40) cc_final: 0.8426 (tp-100) REVERT: B 382 ARG cc_start: 0.8608 (mmp80) cc_final: 0.8231 (mmp-170) REVERT: B 383 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8162 (tm-30) REVERT: A 3 ASP cc_start: 0.9018 (t0) cc_final: 0.8709 (t0) REVERT: A 44 ASN cc_start: 0.9217 (p0) cc_final: 0.8842 (p0) REVERT: A 80 LYS cc_start: 0.8455 (mtmm) cc_final: 0.7982 (mtmm) REVERT: A 84 ASP cc_start: 0.7934 (m-30) cc_final: 0.7665 (m-30) REVERT: A 194 LYS cc_start: 0.8884 (mttm) cc_final: 0.8504 (mttm) REVERT: A 198 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.9078 (mp) REVERT: A 234 LEU cc_start: 0.8931 (mm) cc_final: 0.8716 (mm) REVERT: A 252 ARG cc_start: 0.8458 (mmm-85) cc_final: 0.7979 (mmt90) REVERT: A 288 ILE cc_start: 0.8591 (tp) cc_final: 0.8331 (tp) REVERT: A 327 ARG cc_start: 0.7551 (ttp-170) cc_final: 0.7268 (ttp-170) REVERT: A 345 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8211 (mm-30) REVERT: A 356 ARG cc_start: 0.7761 (mmt-90) cc_final: 0.7228 (mmt-90) REVERT: A 365 GLN cc_start: 0.8930 (tp40) cc_final: 0.8511 (tp-100) REVERT: A 380 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8463 (pp30) REVERT: C 3 ASP cc_start: 0.8613 (t0) cc_final: 0.8371 (t0) REVERT: C 80 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8174 (mtmm) REVERT: C 164 GLU cc_start: 0.6772 (tt0) cc_final: 0.5814 (mt-10) REVERT: C 165 GLN cc_start: 0.3000 (OUTLIER) cc_final: 0.2613 (mt0) REVERT: C 173 HIS cc_start: 0.7878 (t-90) cc_final: 0.7669 (t-90) REVERT: C 194 LYS cc_start: 0.8613 (mttm) cc_final: 0.8283 (mttm) REVERT: C 198 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9126 (mp) REVERT: C 247 LEU cc_start: 0.9047 (tp) cc_final: 0.8832 (tp) REVERT: C 250 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8630 (tt) REVERT: C 252 ARG cc_start: 0.8337 (mmt90) cc_final: 0.7981 (mmt90) REVERT: C 255 LYS cc_start: 0.2661 (mmtt) cc_final: 0.1917 (mmtt) REVERT: C 308 THR cc_start: 0.7068 (OUTLIER) cc_final: 0.6730 (m) REVERT: C 345 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8287 (mm-30) REVERT: C 356 ARG cc_start: 0.7546 (mmt-90) cc_final: 0.6850 (mmt-90) REVERT: C 365 GLN cc_start: 0.8797 (tp40) cc_final: 0.8594 (tp40) REVERT: C 380 GLN cc_start: 0.8765 (tp-100) cc_final: 0.8498 (tp-100) REVERT: C 383 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8054 (tm-30) outliers start: 48 outliers final: 29 residues processed: 387 average time/residue: 0.1262 time to fit residues: 64.8815 Evaluate side-chains 377 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 342 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 380 GLN Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 385 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 HIS ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.170273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.144693 restraints weight = 19443.775| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 3.73 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3981 r_free = 0.3981 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3980 r_free = 0.3980 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 1.0563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.141 10450 Z= 0.492 Angle : 1.809 45.621 14404 Z= 0.931 Chirality : 0.234 4.580 1722 Planarity : 0.008 0.076 1632 Dihedral : 21.945 179.101 1932 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 49.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.18 % Allowed : 27.22 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.25), residues: 1125 helix: 0.45 (0.19), residues: 711 sheet: -2.32 (0.81), residues: 30 loop : -1.16 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG C 157 TYR 0.032 0.003 TYR B 323 PHE 0.090 0.003 PHE C 184 TRP 0.007 0.001 TRP C 174 HIS 0.007 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00805 / 0.49 (10450) covalent geometry : angle 1.80919 / 0.93 (14404) hydrogen bonds : bond 0.53445 / 35.58 ( 651) hydrogen bonds : angle 5.43418 / 3.90 ( 1719) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 347 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 TYR cc_start: 0.6293 (m-80) cc_final: 0.6065 (m-80) REVERT: B 80 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8123 (mtmm) REVERT: B 173 HIS cc_start: 0.7644 (t-90) cc_final: 0.7411 (t-90) REVERT: B 180 MET cc_start: 0.9008 (mtm) cc_final: 0.8798 (mpp) REVERT: B 257 LYS cc_start: 0.9033 (tppp) cc_final: 0.8805 (mmtp) REVERT: B 259 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8009 (mm-30) REVERT: B 336 LYS cc_start: 0.9213 (mptt) cc_final: 0.8972 (mmtp) REVERT: B 345 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7747 (mm-30) REVERT: B 357 LYS cc_start: 0.8751 (ptpp) cc_final: 0.8538 (mtmm) REVERT: B 382 ARG cc_start: 0.8643 (mmp80) cc_final: 0.8266 (mmp-170) REVERT: B 383 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8172 (tm-30) REVERT: A 3 ASP cc_start: 0.9030 (t0) cc_final: 0.8713 (t0) REVERT: A 47 ILE cc_start: 0.9097 (mm) cc_final: 0.8841 (mp) REVERT: A 80 LYS cc_start: 0.8435 (mtmm) cc_final: 0.7970 (mtmm) REVERT: A 84 ASP cc_start: 0.7993 (m-30) cc_final: 0.7735 (m-30) REVERT: A 194 LYS cc_start: 0.8927 (mttm) cc_final: 0.8257 (mttm) REVERT: A 198 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.9079 (mp) REVERT: A 234 LEU cc_start: 0.8945 (mm) cc_final: 0.8725 (mm) REVERT: A 247 LEU cc_start: 0.9090 (tp) cc_final: 0.8810 (tp) REVERT: A 252 ARG cc_start: 0.8458 (mmm-85) cc_final: 0.7943 (mmt90) REVERT: A 288 ILE cc_start: 0.8558 (tp) cc_final: 0.8269 (tp) REVERT: A 345 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8287 (mm-30) REVERT: A 354 GLU cc_start: 0.8394 (tp30) cc_final: 0.8133 (pt0) REVERT: A 356 ARG cc_start: 0.7656 (mmt-90) cc_final: 0.7167 (mmt-90) REVERT: A 365 GLN cc_start: 0.8999 (tp40) cc_final: 0.8550 (tp-100) REVERT: C 3 ASP cc_start: 0.8606 (t0) cc_final: 0.8354 (t0) REVERT: C 80 LYS cc_start: 0.8580 (mtmm) cc_final: 0.7910 (mtmm) REVERT: C 84 ASP cc_start: 0.8172 (m-30) cc_final: 0.7910 (m-30) REVERT: C 165 GLN cc_start: 0.2381 (OUTLIER) cc_final: 0.2160 (mt0) REVERT: C 173 HIS cc_start: 0.7845 (t-90) cc_final: 0.7634 (t-90) REVERT: C 180 MET cc_start: 0.8664 (mpp) cc_final: 0.8462 (mpp) REVERT: C 194 LYS cc_start: 0.8716 (mttm) cc_final: 0.8207 (mttm) REVERT: C 198 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9142 (mp) REVERT: C 247 LEU cc_start: 0.9087 (tp) cc_final: 0.8828 (tp) REVERT: C 250 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8647 (tt) REVERT: C 252 ARG cc_start: 0.8372 (mmt90) cc_final: 0.7980 (mmt90) REVERT: C 255 LYS cc_start: 0.2955 (mmtt) cc_final: 0.2059 (mmtt) REVERT: C 308 THR cc_start: 0.6942 (OUTLIER) cc_final: 0.6717 (m) REVERT: C 345 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8302 (mm-30) REVERT: C 356 ARG cc_start: 0.7644 (mmt-90) cc_final: 0.6896 (mmt-90) REVERT: C 382 ARG cc_start: 0.8595 (mmp80) cc_final: 0.8130 (mmp80) outliers start: 41 outliers final: 29 residues processed: 366 average time/residue: 0.1207 time to fit residues: 58.7495 Evaluate side-chains 364 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 330 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 385 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 49 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 83 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 165 GLN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 ASN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.173935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.147940 restraints weight = 19387.071| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.83 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4020 r_free = 0.4020 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4021 r_free = 0.4021 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.4021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 1.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.131 10450 Z= 0.465 Angle : 1.780 40.854 14404 Z= 0.918 Chirality : 0.232 4.610 1722 Planarity : 0.008 0.081 1632 Dihedral : 22.252 178.184 1932 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 47.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.04 % Favored : 93.87 % Rotamer: Outliers : 2.85 % Allowed : 28.64 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.25), residues: 1125 helix: 0.16 (0.19), residues: 741 sheet: -2.25 (0.82), residues: 30 loop : -0.93 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 157 TYR 0.029 0.003 TYR C 211 PHE 0.078 0.003 PHE C 184 TRP 0.007 0.001 TRP C 174 HIS 0.007 0.001 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.46 (10450) covalent geometry : angle 1.77999 / 0.92 (14404) hydrogen bonds : bond 0.52682 / 35.11 ( 651) hydrogen bonds : angle 5.41216 / 3.88 ( 1719) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 342 time to evaluate : 0.271 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: B 80 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8138 (mtmm) REVERT: B 118 LYS cc_start: 0.8691 (mmmt) cc_final: 0.8295 (ptpp) REVERT: B 133 PHE cc_start: 0.8685 (t80) cc_final: 0.8483 (t80) REVERT: B 173 HIS cc_start: 0.7652 (t-90) cc_final: 0.7439 (t-90) REVERT: B 257 LYS cc_start: 0.8957 (tppp) cc_final: 0.8737 (mmtp) REVERT: B 259 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7884 (mm-30) REVERT: B 336 LYS cc_start: 0.9196 (mptt) cc_final: 0.8980 (mmtp) REVERT: B 345 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7764 (mm-30) REVERT: B 382 ARG cc_start: 0.8720 (mmp80) cc_final: 0.8394 (mmp-170) REVERT: B 383 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8141 (tm-30) REVERT: A 3 ASP cc_start: 0.9044 (t0) cc_final: 0.8724 (t0) REVERT: A 47 ILE cc_start: 0.9103 (mm) cc_final: 0.8854 (mp) REVERT: A 80 LYS cc_start: 0.8412 (mtmm) cc_final: 0.7946 (mtmm) REVERT: A 84 ASP cc_start: 0.7977 (m-30) cc_final: 0.7716 (m-30) REVERT: A 194 LYS cc_start: 0.8890 (mttm) cc_final: 0.8487 (mttm) REVERT: A 198 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.9035 (mp) REVERT: A 234 LEU cc_start: 0.8874 (mm) cc_final: 0.8641 (mm) REVERT: A 252 ARG cc_start: 0.8431 (mmm-85) cc_final: 0.7940 (mmt90) REVERT: A 259 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7781 (tp30) REVERT: A 288 ILE cc_start: 0.8651 (tp) cc_final: 0.8402 (tp) REVERT: A 345 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8226 (mm-30) REVERT: A 354 GLU cc_start: 0.8378 (tp30) cc_final: 0.7996 (pt0) REVERT: A 356 ARG cc_start: 0.7645 (mmt-90) cc_final: 0.6991 (mmt-90) REVERT: A 360 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7943 (mt-10) REVERT: C 3 ASP cc_start: 0.8613 (t0) cc_final: 0.8367 (t0) REVERT: C 47 ILE cc_start: 0.9140 (mm) cc_final: 0.8779 (mp) REVERT: C 80 LYS cc_start: 0.8594 (mtmm) cc_final: 0.7950 (mtmm) REVERT: C 81 TYR cc_start: 0.8524 (t80) cc_final: 0.8198 (t80) REVERT: C 84 ASP cc_start: 0.8139 (m-30) cc_final: 0.7870 (m-30) REVERT: C 133 PHE cc_start: 0.8669 (t80) cc_final: 0.8467 (t80) REVERT: C 173 HIS cc_start: 0.7792 (t-90) cc_final: 0.7571 (t-90) REVERT: C 194 LYS cc_start: 0.8602 (mttm) cc_final: 0.8327 (mttm) REVERT: C 198 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9138 (mp) REVERT: C 250 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8635 (tt) REVERT: C 252 ARG cc_start: 0.8345 (mmt90) cc_final: 0.8100 (mmt90) REVERT: C 255 LYS cc_start: 0.2992 (mmtt) cc_final: 0.2096 (mmtt) REVERT: C 345 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8280 (mm-30) REVERT: C 354 GLU cc_start: 0.8908 (tp30) cc_final: 0.7903 (tp30) REVERT: C 356 ARG cc_start: 0.7514 (mmt-90) cc_final: 0.6811 (mmt-90) REVERT: C 357 LYS cc_start: 0.8719 (mtmm) cc_final: 0.8302 (mtmm) REVERT: C 380 GLN cc_start: 0.8756 (tp-100) cc_final: 0.8426 (tp-100) REVERT: C 382 ARG cc_start: 0.8628 (mmp80) cc_final: 0.8149 (mmp80) outliers start: 28 outliers final: 22 residues processed: 357 average time/residue: 0.1258 time to fit residues: 59.5140 Evaluate side-chains 350 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 325 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 323 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 95 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 113 optimal weight: 0.3980 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.174294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.148230 restraints weight = 19576.030| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.84 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4030 r_free = 0.4030 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (15 function evaluations) r_final: 0.4031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 1.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.128 10450 Z= 0.452 Angle : 1.719 36.018 14404 Z= 0.896 Chirality : 0.228 4.620 1722 Planarity : 0.009 0.202 1632 Dihedral : 22.532 179.637 1932 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 47.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.06 % Allowed : 29.66 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.25), residues: 1125 helix: 0.21 (0.19), residues: 723 sheet: -2.24 (0.81), residues: 30 loop : -1.01 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 382 TYR 0.031 0.003 TYR A 65 PHE 0.066 0.003 PHE C 184 TRP 0.007 0.001 TRP C 174 HIS 0.014 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.45 (10450) covalent geometry : angle 1.71870 / 0.90 (14404) hydrogen bonds : bond 0.51741 / 34.51 ( 651) hydrogen bonds : angle 5.51284 / 3.94 ( 1719) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2762.45 seconds wall clock time: 48 minutes 36.92 seconds (2916.92 seconds total)