Starting phenix.real_space_refine on Wed Mar 4 17:02:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sxo_10344/03_2026/6sxo_10344.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sxo_10344/03_2026/6sxo_10344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sxo_10344/03_2026/6sxo_10344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sxo_10344/03_2026/6sxo_10344.map" model { file = "/net/cci-nas-00/data/ceres_data/6sxo_10344/03_2026/6sxo_10344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sxo_10344/03_2026/6sxo_10344.cif" } resolution = 3.3 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= 0.003 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 326 5.49 5 S 32 5.16 5 C 8094 2.51 5 N 2786 2.21 5 O 3656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14894 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2931 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 12, 'TRANS': 362} Chain: "Lh" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Lk" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "LR" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1281 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 3, 'TRANS': 149} Chain: "LX" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 985 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "LY" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "L5" Number of atoms: 5761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 5761 Classifications: {'RNA': 268} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 15, 'rna3p_pur': 135, 'rna3p_pyr': 105} Link IDs: {'rna2p': 28, 'rna3p': 239} Chain breaks: 6 Chain: "L8" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1237 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 3, 'rna3p_pur': 22, 'rna3p_pyr': 23} Link IDs: {'rna2p': 13, 'rna3p': 44} Time building chain proxies: 3.01, per 1000 atoms: 0.20 Number of scatterers: 14894 At special positions: 0 Unit cell: (155.15, 212.93, 126.26, 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 32 16.00 P 326 15.00 O 3656 8.00 N 2786 7.00 C 8094 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: 0.85 Conformation dependent library (CDL) restraints added in 374.9 milliseconds 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 11 sheets defined 43.7% alpha, 13.3% beta 98 base pairs and 176 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.881A pdb=" N VAL A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 27 " --> pdb=" O MET A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 63 Processing helix chain 'A' and resid 136 through 157 removed outlier: 3.522A pdb=" N VAL A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 177 removed outlier: 4.394A pdb=" N VAL A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 285 through 299 removed outlier: 3.871A pdb=" N ALA A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.608A pdb=" N LEU A 342 " --> pdb=" O GLU A 339 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 343 " --> pdb=" O PRO A 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 339 through 343' Processing helix chain 'A' and resid 351 through 361 removed outlier: 4.026A pdb=" N SER A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.672A pdb=" N ALA A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 5 through 10 removed outlier: 3.565A pdb=" N ARGLh 10 " --> pdb=" O ALALh 6 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 13 through 34 removed outlier: 3.567A pdb=" N ASPLh 23 " --> pdb=" O LYSLh 19 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEULh 24 " --> pdb=" O GLNLh 20 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VALLh 26 " --> pdb=" O ASPLh 22 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEULh 28 " --> pdb=" O LEULh 24 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SERLh 29 " --> pdb=" O LYSLh 25 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 40 through 45 Processing helix chain 'Lh' and resid 46 through 73 removed outlier: 3.662A pdb=" N ARGLh 56 " --> pdb=" O LYSLh 52 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THRLh 64 " --> pdb=" O VALLh 60 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 98 through 102 removed outlier: 4.176A pdb=" N ASNLh 101 " --> pdb=" O HISLh 98 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEULh 102 " --> pdb=" O GLULh 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lh' and resid 98 through 102' Processing helix chain 'Lh' and resid 106 through 114 removed outlier: 3.768A pdb=" N ARGLh 112 " --> pdb=" O GLNLh 108 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYRLh 114 " --> pdb=" O LYSLh 110 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 8 through 16 removed outlier: 3.538A pdb=" N LEULk 12 " --> pdb=" O ILELk 8 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEULk 13 " --> pdb=" O LYSLk 9 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THRLk 14 " --> pdb=" O ASPLk 10 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 49 through 59 removed outlier: 3.571A pdb=" N GLULk 54 " --> pdb=" O LYSLk 50 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYSLk 55 " --> pdb=" O GLULk 51 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLNLk 58 " --> pdb=" O GLULk 54 " (cutoff:3.500A) Processing helix chain 'LR' and resid 4 through 15 Processing helix chain 'LR' and resid 18 through 20 No H-bonds generated for 'chain 'LR' and resid 18 through 20' Processing helix chain 'LR' and resid 28 through 34 removed outlier: 3.591A pdb=" N ILELR 32 " --> pdb=" O GLULR 28 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASNLR 34 " --> pdb=" O ASNLR 30 " (cutoff:3.500A) Processing helix chain 'LR' and resid 37 through 47 removed outlier: 3.740A pdb=" N LEULR 44 " --> pdb=" O GLNLR 40 " (cutoff:3.500A) Processing helix chain 'LR' and resid 60 through 71 removed outlier: 3.806A pdb=" N LYSLR 65 " --> pdb=" O ALALR 61 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASNLR 66 " --> pdb=" O ARGLR 62 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THRLR 67 " --> pdb=" O CYSLR 63 " (cutoff:3.500A) Processing helix chain 'LR' and resid 84 through 89 removed outlier: 3.704A pdb=" N METLR 89 " --> pdb=" O ALALR 85 " (cutoff:3.500A) Processing helix chain 'LR' and resid 90 through 112 removed outlier: 3.623A pdb=" N TRPLR 95 " --> pdb=" O GLULR 91 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARGLR 100 " --> pdb=" O METLR 96 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGLR 110 " --> pdb=" O LEULR 106 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLULR 111 " --> pdb=" O ARGLR 107 " (cutoff:3.500A) Processing helix chain 'LR' and resid 116 through 129 removed outlier: 4.504A pdb=" N SERLR 122 " --> pdb=" O HISLR 118 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEULR 125 " --> pdb=" O HISLR 121 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLYLR 129 " --> pdb=" O LEULR 125 " (cutoff:3.500A) Processing helix chain 'LR' and resid 134 through 150 removed outlier: 4.835A pdb=" N GLULR 140 " --> pdb=" O ARGLR 136 " (cutoff:3.500A) Processing helix chain 'LX' and resid 72 through 76 Processing helix chain 'LX' and resid 105 through 118 Processing helix chain 'LX' and resid 145 through 154 Processing helix chain 'LY' and resid 10 through 20 removed outlier: 3.597A pdb=" N HISLY 18 " --> pdb=" O ASNLY 14 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASNLY 20 " --> pdb=" O LYSLY 16 " (cutoff:3.500A) Processing helix chain 'LY' and resid 24 through 30 removed outlier: 4.094A pdb=" N LYSLY 28 " --> pdb=" O HISLY 24 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N METLY 30 " --> pdb=" O ARGLY 26 " (cutoff:3.500A) Processing helix chain 'LY' and resid 37 through 42 removed outlier: 3.543A pdb=" N TYRLY 42 " --> pdb=" O LEULY 38 " (cutoff:3.500A) Processing helix chain 'LY' and resid 75 through 78 Processing helix chain 'LY' and resid 100 through 102 No H-bonds generated for 'chain 'LY' and resid 100 through 102' Processing helix chain 'LY' and resid 112 through 129 removed outlier: 3.503A pdb=" N LYSLY 117 " --> pdb=" O LYSLY 113 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILELY 118 " --> pdb=" O ASPLY 114 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALALY 123 " --> pdb=" O LEULY 119 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SERLY 125 " --> pdb=" O ARGLY 121 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARGLY 126 " --> pdb=" O LYSLY 122 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLNLY 127 " --> pdb=" O ALALY 123 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VALLY 128 " --> pdb=" O LYSLY 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 81 removed outlier: 5.747A pdb=" N ALA A 75 " --> pdb=" O HIS A 113 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N HIS A 113 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY A 111 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A 107 " --> pdb=" O SER A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 181 removed outlier: 4.478A pdb=" N VAL A 223 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 187 removed outlier: 4.326A pdb=" N MET A 185 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 203 " --> pdb=" O MET A 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 279 Processing sheet with id=AA6, first strand: chain 'Lk' and resid 4 through 5 removed outlier: 4.421A pdb=" N VALLk 46 " --> pdb=" O ILELk 5 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SERLk 22 " --> pdb=" O ARGLk 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'LR' and resid 22 through 23 Processing sheet with id=AA8, first strand: chain 'LX' and resid 77 through 80 removed outlier: 3.609A pdb=" N PHELX 79 " --> pdb=" O ILELX 99 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYSLX 134 " --> pdb=" O VALLX 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'LX' and resid 121 through 123 Processing sheet with id=AB1, first strand: chain 'LY' and resid 31 through 33 Processing sheet with id=AB2, first strand: chain 'LY' and resid 94 through 99 removed outlier: 3.861A pdb=" N VALLY 97 " --> pdb=" O VALLY 85 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VALLY 85 " --> pdb=" O VALLY 97 " (cutoff:3.500A) removed outlier: 11.462A pdb=" N ILELY 99 " --> pdb=" O GLULY 83 " (cutoff:3.500A) removed outlier: 10.812A pdb=" N GLULY 83 " --> pdb=" O ILELY 99 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLNLY 72 " --> pdb=" O TYRLY 81 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLULY 83 " --> pdb=" O VALLY 70 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N VALLY 70 " --> pdb=" O GLULY 83 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VALLY 85 " --> pdb=" O GLYLY 68 " (cutoff:3.500A) removed outlier: 10.148A pdb=" N GLYLY 68 " --> pdb=" O VALLY 85 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 257 hydrogen bonds 436 hydrogen bond angles 0 basepair planarities 98 basepair parallelities 176 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2201 1.32 - 1.44: 5593 1.44 - 1.57: 7333 1.57 - 1.69: 647 1.69 - 1.81: 55 Bond restraints: 15829 Sorted by residual: bond pdb=" C1' CL53241 " pdb=" N1 CL53241 " ideal model delta sigma weight residual 1.480 1.558 -0.078 1.50e-02 4.44e+03 2.67e+01 bond pdb=" C1' CL53579 " pdb=" N1 CL53579 " ideal model delta sigma weight residual 1.470 1.513 -0.043 1.50e-02 4.44e+03 8.03e+00 bond pdb=" CG LEULk 69 " pdb=" CD1 LEULk 69 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.94e+00 bond pdb=" CG LEULR 15 " pdb=" CD1 LEULR 15 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.29e+00 bond pdb=" CB ARGLh 7 " pdb=" CG ARGLh 7 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.22e+00 ... (remaining 15824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 22224 3.49 - 6.98: 556 6.98 - 10.46: 78 10.46 - 13.95: 10 13.95 - 17.44: 3 Bond angle restraints: 22871 Sorted by residual: angle pdb=" O3' CL53294 " pdb=" P GL53295 " pdb=" O5' GL53295 " ideal model delta sigma weight residual 104.00 119.07 -15.07 1.50e+00 4.44e-01 1.01e+02 angle pdb=" P GL53295 " pdb=" O5' GL53295 " pdb=" C5' GL53295 " ideal model delta sigma weight residual 120.90 133.63 -12.73 1.50e+00 4.44e-01 7.20e+01 angle pdb=" O3' UL53583 " pdb=" P CL53584 " pdb=" O5' CL53584 " ideal model delta sigma weight residual 104.00 115.57 -11.57 1.50e+00 4.44e-01 5.95e+01 angle pdb=" C3' UL53583 " pdb=" O3' UL53583 " pdb=" P CL53584 " ideal model delta sigma weight residual 120.20 131.51 -11.31 1.50e+00 4.44e-01 5.68e+01 angle pdb=" C3' GL53256 " pdb=" O3' GL53256 " pdb=" P GL53257 " ideal model delta sigma weight residual 120.20 130.53 -10.33 1.50e+00 4.44e-01 4.75e+01 ... (remaining 22866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 9300 34.97 - 69.94: 852 69.94 - 104.91: 121 104.91 - 139.88: 8 139.88 - 174.85: 9 Dihedral angle restraints: 10290 sinusoidal: 7437 harmonic: 2853 Sorted by residual: dihedral pdb=" O4' CL52709 " pdb=" C1' CL52709 " pdb=" N1 CL52709 " pdb=" C2 CL52709 " ideal model delta sinusoidal sigma weight residual -160.00 -29.77 -130.23 1 1.50e+01 4.44e-03 7.02e+01 dihedral pdb=" O4' UL8 51 " pdb=" C1' UL8 51 " pdb=" N1 UL8 51 " pdb=" C2 UL8 51 " ideal model delta sinusoidal sigma weight residual 232.00 57.15 174.85 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' UL52707 " pdb=" C1' UL52707 " pdb=" N1 UL52707 " pdb=" C2 UL52707 " ideal model delta sinusoidal sigma weight residual -128.00 38.07 -166.07 1 1.70e+01 3.46e-03 6.55e+01 ... (remaining 10287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2608 0.111 - 0.222: 183 0.222 - 0.333: 16 0.333 - 0.443: 3 0.443 - 0.554: 4 Chirality restraints: 2814 Sorted by residual: chirality pdb=" C4' CL52943 " pdb=" C5' CL52943 " pdb=" O4' CL52943 " pdb=" C3' CL52943 " both_signs ideal model delta sigma weight residual False -2.50 -1.94 -0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" CB ILELh 4 " pdb=" CA ILELh 4 " pdb=" CG1 ILELh 4 " pdb=" CG2 ILELh 4 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" P GL53580 " pdb=" OP1 GL53580 " pdb=" OP2 GL53580 " pdb=" O5' GL53580 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 2811 not shown) Planarity restraints: 1675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' UL52932 " -0.024 2.00e-02 2.50e+03 2.23e-02 1.12e+01 pdb=" N1 UL52932 " 0.053 2.00e-02 2.50e+03 pdb=" C2 UL52932 " -0.029 2.00e-02 2.50e+03 pdb=" O2 UL52932 " 0.009 2.00e-02 2.50e+03 pdb=" N3 UL52932 " 0.004 2.00e-02 2.50e+03 pdb=" C4 UL52932 " -0.004 2.00e-02 2.50e+03 pdb=" O4 UL52932 " -0.004 2.00e-02 2.50e+03 pdb=" C5 UL52932 " 0.004 2.00e-02 2.50e+03 pdb=" C6 UL52932 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CL52942 " 0.038 2.00e-02 2.50e+03 2.17e-02 1.06e+01 pdb=" N1 CL52942 " -0.046 2.00e-02 2.50e+03 pdb=" C2 CL52942 " 0.010 2.00e-02 2.50e+03 pdb=" O2 CL52942 " -0.011 2.00e-02 2.50e+03 pdb=" N3 CL52942 " 0.008 2.00e-02 2.50e+03 pdb=" C4 CL52942 " 0.002 2.00e-02 2.50e+03 pdb=" N4 CL52942 " 0.004 2.00e-02 2.50e+03 pdb=" C5 CL52942 " 0.011 2.00e-02 2.50e+03 pdb=" C6 CL52942 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GL52941 " -0.013 2.00e-02 2.50e+03 1.87e-02 1.05e+01 pdb=" N9 GL52941 " 0.051 2.00e-02 2.50e+03 pdb=" C8 GL52941 " -0.007 2.00e-02 2.50e+03 pdb=" N7 GL52941 " -0.002 2.00e-02 2.50e+03 pdb=" C5 GL52941 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GL52941 " -0.002 2.00e-02 2.50e+03 pdb=" O6 GL52941 " 0.001 2.00e-02 2.50e+03 pdb=" N1 GL52941 " 0.006 2.00e-02 2.50e+03 pdb=" C2 GL52941 " 0.001 2.00e-02 2.50e+03 pdb=" N2 GL52941 " 0.004 2.00e-02 2.50e+03 pdb=" N3 GL52941 " -0.004 2.00e-02 2.50e+03 pdb=" C4 GL52941 " -0.036 2.00e-02 2.50e+03 ... (remaining 1672 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3156 2.78 - 3.31: 12283 3.31 - 3.84: 27225 3.84 - 4.37: 32008 4.37 - 4.90: 45682 Nonbonded interactions: 120354 Sorted by model distance: nonbonded pdb=" O6 GL52950 " pdb=" O4 UL53244 " model vdw 2.255 2.432 nonbonded pdb=" O6 GL8 60 " pdb=" O2' CL8 96 " model vdw 2.264 3.040 nonbonded pdb=" N2 GL52941 " pdb=" O2 CL53254 " model vdw 2.270 3.120 nonbonded pdb=" O2' AL8 48 " pdb=" OP2 CL8 50 " model vdw 2.278 3.040 nonbonded pdb=" O2' AL5 410 " pdb=" O2' CL5 414 " model vdw 2.282 3.040 ... (remaining 120349 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 10.780 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.580 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 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 : 0.009 0.087 15829 Z= 0.425 Angle : 1.352 17.441 22871 Z= 0.700 Chirality : 0.066 0.554 2814 Planarity : 0.007 0.058 1675 Dihedral : 22.524 174.846 8430 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.16 % Allowed : 5.33 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.39 (0.20), residues: 961 helix: -3.72 (0.16), residues: 386 sheet: -1.40 (0.45), residues: 115 loop : -2.50 (0.21), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARGLh 7 TYR 0.032 0.004 TYRLY 74 PHE 0.032 0.004 PHELR 132 TRP 0.013 0.003 TRPLR 23 HIS 0.034 0.004 HISLR 143 Details of bonding type rmsd covalent geometry : bond 0.00874 (15829) covalent geometry : angle 1.35230 (22871) hydrogen bonds : bond 0.20558 ( 551) hydrogen bonds : angle 7.26496 ( 1282) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 248 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.6803 (mmtt) cc_final: 0.6376 (mmtm) REVERT: Lk 40 ARG cc_start: 0.7638 (ttt90) cc_final: 0.7411 (ttt-90) REVERT: LR 27 ASN cc_start: 0.7847 (m-40) cc_final: 0.7587 (m-40) REVERT: LR 88 ARG cc_start: 0.8292 (mtp180) cc_final: 0.6700 (mmt-90) REVERT: LR 89 MET cc_start: 0.7736 (tpp) cc_final: 0.7353 (tpt) REVERT: LR 96 MET cc_start: 0.6948 (tmt) cc_final: 0.6597 (ttt) REVERT: LX 50 LYS cc_start: 0.7904 (ptmt) cc_final: 0.7655 (tptp) REVERT: LX 53 ARG cc_start: 0.7869 (mtt180) cc_final: 0.6562 (mtt-85) REVERT: LX 69 ASN cc_start: 0.7599 (t0) cc_final: 0.6835 (t0) REVERT: LX 133 GLU cc_start: 0.7682 (mp0) cc_final: 0.7444 (mp0) outliers start: 10 outliers final: 2 residues processed: 255 average time/residue: 0.1667 time to fit residues: 56.6393 Evaluate side-chains 160 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LY residue 79 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.0030 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 84 ASN A 123 HIS ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS A 209 GLN A 213 HIS Lh 20 GLN LR 130 ASN LR 143 HIS LX 73 HIS LX 108 GLN LY 4 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.199794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.164296 restraints weight = 29487.144| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.56 r_work: 0.3645 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15829 Z= 0.138 Angle : 0.700 9.539 22871 Z= 0.351 Chirality : 0.039 0.261 2814 Planarity : 0.005 0.039 1675 Dihedral : 24.072 172.329 6263 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.90 % Allowed : 9.85 % Favored : 87.25 % 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: -2.85 (0.23), residues: 961 helix: -2.00 (0.22), residues: 406 sheet: -1.06 (0.46), residues: 117 loop : -1.91 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGLh 7 TYR 0.015 0.001 TYRLY 74 PHE 0.011 0.001 PHELR 132 TRP 0.012 0.002 TRPLR 95 HIS 0.011 0.001 HISLR 143 Details of bonding type rmsd covalent geometry : bond 0.00276 (15829) covalent geometry : angle 0.69980 (22871) hydrogen bonds : bond 0.07170 ( 551) hydrogen bonds : angle 4.27258 ( 1282) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.6998 (mmtt) cc_final: 0.6730 (mmtp) REVERT: A 320 LYS cc_start: 0.6741 (ttmt) cc_final: 0.6487 (tttt) REVERT: A 326 MET cc_start: 0.4633 (mmm) cc_final: 0.4018 (mmm) REVERT: A 331 MET cc_start: 0.1282 (ttp) cc_final: -0.0746 (mtt) REVERT: LR 34 ASN cc_start: 0.7784 (p0) cc_final: 0.7538 (p0) REVERT: LR 88 ARG cc_start: 0.8260 (mtp180) cc_final: 0.6416 (mmp-170) REVERT: LR 89 MET cc_start: 0.8076 (tpp) cc_final: 0.7683 (tpt) REVERT: LR 96 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7536 (ttt) REVERT: LX 50 LYS cc_start: 0.8281 (ptmt) cc_final: 0.7721 (tptp) REVERT: LX 69 ASN cc_start: 0.7840 (t0) cc_final: 0.7188 (t0) REVERT: LX 131 ASP cc_start: 0.7391 (t0) cc_final: 0.6881 (t0) REVERT: LY 16 LYS cc_start: 0.9054 (tttm) cc_final: 0.8437 (mptt) REVERT: LY 36 LYS cc_start: 0.7406 (mttm) cc_final: 0.7203 (mttm) outliers start: 25 outliers final: 12 residues processed: 218 average time/residue: 0.1291 time to fit residues: 39.8723 Evaluate side-chains 173 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain LR residue 15 LEU Chi-restraints excluded: chain LR residue 96 MET Chi-restraints excluded: chain LR residue 130 ASN Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LY residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 75 optimal weight: 0.0020 chunk 78 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 359 GLN Lh 20 GLN LR 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.196338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.158488 restraints weight = 29819.782| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.97 r_work: 0.3579 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15829 Z= 0.191 Angle : 0.686 9.463 22871 Z= 0.343 Chirality : 0.040 0.254 2814 Planarity : 0.005 0.043 1675 Dihedral : 23.883 169.808 6261 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.82 % Allowed : 11.82 % Favored : 84.36 % 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: -2.23 (0.24), residues: 961 helix: -1.41 (0.24), residues: 403 sheet: -0.97 (0.47), residues: 115 loop : -1.57 (0.25), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGLR 62 TYR 0.020 0.002 TYRLY 74 PHE 0.013 0.002 PHE A 117 TRP 0.012 0.002 TRPLR 95 HIS 0.006 0.002 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00398 (15829) covalent geometry : angle 0.68642 (22871) hydrogen bonds : bond 0.07152 ( 551) hydrogen bonds : angle 4.02088 ( 1282) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7439 (mmtt) cc_final: 0.7101 (mmtp) REVERT: A 320 LYS cc_start: 0.6865 (ttmt) cc_final: 0.6628 (mttt) REVERT: A 331 MET cc_start: 0.1732 (ttp) cc_final: 0.0288 (mtt) REVERT: LR 34 ASN cc_start: 0.8020 (p0) cc_final: 0.7731 (p0) REVERT: LR 88 ARG cc_start: 0.8370 (mtp180) cc_final: 0.6289 (mmp-170) REVERT: LR 96 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7937 (ttt) REVERT: LX 50 LYS cc_start: 0.8434 (ptmt) cc_final: 0.7755 (tptp) REVERT: LX 69 ASN cc_start: 0.7958 (t0) cc_final: 0.7344 (t0) REVERT: LX 133 GLU cc_start: 0.8667 (mp0) cc_final: 0.8229 (mp0) REVERT: LY 84 ARG cc_start: 0.7921 (mpp80) cc_final: 0.7629 (mtm-85) REVERT: LY 117 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8146 (mtmm) outliers start: 33 outliers final: 20 residues processed: 176 average time/residue: 0.1358 time to fit residues: 33.7030 Evaluate side-chains 165 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LR residue 96 MET Chi-restraints excluded: chain LR residue 145 LEU Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LY residue 117 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 19 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 chunk 96 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Lh 20 GLN LR 7 GLN LX 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.197924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.159847 restraints weight = 29691.748| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 3.08 r_work: 0.3597 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15829 Z= 0.137 Angle : 0.607 8.771 22871 Z= 0.305 Chirality : 0.037 0.232 2814 Planarity : 0.004 0.043 1675 Dihedral : 23.713 171.137 6261 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.36 % Allowed : 13.21 % Favored : 83.43 % 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: -1.77 (0.25), residues: 961 helix: -0.90 (0.25), residues: 401 sheet: -0.92 (0.47), residues: 115 loop : -1.40 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGLR 16 TYR 0.017 0.001 TYRLY 74 PHE 0.009 0.001 PHE A 117 TRP 0.008 0.001 TRPLR 95 HIS 0.005 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00279 (15829) covalent geometry : angle 0.60736 (22871) hydrogen bonds : bond 0.06335 ( 551) hydrogen bonds : angle 3.73681 ( 1282) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7705 (t) REVERT: A 311 LYS cc_start: 0.7465 (mmtt) cc_final: 0.7129 (mmtp) REVERT: A 331 MET cc_start: 0.1824 (ttp) cc_final: 0.0183 (mtt) REVERT: Lh 87 LYS cc_start: 0.5808 (mmmt) cc_final: 0.5044 (mmmt) REVERT: LR 88 ARG cc_start: 0.8300 (mtp180) cc_final: 0.6342 (mmp-170) REVERT: LR 96 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8091 (ttt) REVERT: LX 50 LYS cc_start: 0.8370 (ptmt) cc_final: 0.7715 (tptp) REVERT: LX 69 ASN cc_start: 0.7936 (t0) cc_final: 0.7335 (t0) REVERT: LY 84 ARG cc_start: 0.7885 (mpp80) cc_final: 0.7668 (mtm-85) REVERT: LY 117 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8221 (mtmm) outliers start: 29 outliers final: 21 residues processed: 180 average time/residue: 0.1234 time to fit residues: 31.8804 Evaluate side-chains 169 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 100 GLU Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LR residue 96 MET Chi-restraints excluded: chain LR residue 145 LEU Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 79 VAL Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LY residue 117 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 72 optimal weight: 0.0050 chunk 76 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 overall best weight: 2.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 178 ASN LR 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.195584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.156439 restraints weight = 29649.555| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.01 r_work: 0.3562 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15829 Z= 0.203 Angle : 0.665 7.416 22871 Z= 0.332 Chirality : 0.039 0.227 2814 Planarity : 0.005 0.045 1675 Dihedral : 23.656 169.471 6261 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.52 % Allowed : 14.14 % Favored : 81.34 % 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: -1.82 (0.25), residues: 961 helix: -0.84 (0.25), residues: 400 sheet: -0.98 (0.47), residues: 115 loop : -1.52 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGLR 16 TYR 0.020 0.002 TYRLY 74 PHE 0.011 0.002 PHE A 177 TRP 0.007 0.001 TRPLR 95 HIS 0.006 0.002 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00425 (15829) covalent geometry : angle 0.66547 (22871) hydrogen bonds : bond 0.06827 ( 551) hydrogen bonds : angle 3.90585 ( 1282) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7789 (t) REVERT: A 163 ASN cc_start: 0.3704 (OUTLIER) cc_final: 0.2720 (m-40) REVERT: A 311 LYS cc_start: 0.7423 (mmtt) cc_final: 0.7149 (mmtp) REVERT: A 331 MET cc_start: 0.2256 (ttp) cc_final: 0.0276 (mtt) REVERT: LR 88 ARG cc_start: 0.8359 (mtp180) cc_final: 0.6379 (mmt180) REVERT: LX 50 LYS cc_start: 0.8420 (ptmt) cc_final: 0.7789 (tptp) REVERT: LX 69 ASN cc_start: 0.8169 (t0) cc_final: 0.7530 (t0) REVERT: LY 84 ARG cc_start: 0.7827 (mpp80) cc_final: 0.7529 (mtm-85) REVERT: LY 117 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8279 (mtmm) outliers start: 39 outliers final: 25 residues processed: 171 average time/residue: 0.1180 time to fit residues: 29.3797 Evaluate side-chains 169 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain Lh residue 15 GLU Chi-restraints excluded: chain Lh residue 18 LEU Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 33 VAL Chi-restraints excluded: chain Lh residue 65 GLN Chi-restraints excluded: chain Lh residue 100 GLU Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 14 THR Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LR residue 145 LEU Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 112 ASP Chi-restraints excluded: chain LY residue 117 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 70 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 HIS ** 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 = 0.4416 r_free = 0.4416 target = 0.197909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.159632 restraints weight = 29500.945| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 3.11 r_work: 0.3594 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15829 Z= 0.129 Angle : 0.587 7.063 22871 Z= 0.295 Chirality : 0.036 0.203 2814 Planarity : 0.004 0.043 1675 Dihedral : 23.567 171.611 6261 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.78 % Allowed : 17.03 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.25), residues: 961 helix: -0.43 (0.26), residues: 400 sheet: -0.97 (0.47), residues: 115 loop : -1.41 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGLR 16 TYR 0.016 0.001 TYRLY 74 PHE 0.010 0.001 PHE A 177 TRP 0.003 0.001 TRPLR 95 HIS 0.004 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00262 (15829) covalent geometry : angle 0.58719 (22871) hydrogen bonds : bond 0.06028 ( 551) hydrogen bonds : angle 3.67386 ( 1282) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 THR cc_start: 0.8085 (m) cc_final: 0.7828 (t) REVERT: A 115 ASP cc_start: 0.5195 (t0) cc_final: 0.4941 (t0) REVERT: A 117 PHE cc_start: 0.6334 (m-80) cc_final: 0.5996 (m-80) REVERT: A 311 LYS cc_start: 0.7538 (mmtt) cc_final: 0.7215 (mmtp) REVERT: A 331 MET cc_start: 0.1966 (ttp) cc_final: 0.0190 (mtt) REVERT: LR 88 ARG cc_start: 0.8343 (mtp180) cc_final: 0.6414 (mmt180) REVERT: LX 50 LYS cc_start: 0.8396 (ptmt) cc_final: 0.7688 (tptp) REVERT: LX 69 ASN cc_start: 0.8016 (t0) cc_final: 0.7384 (t0) REVERT: LY 84 ARG cc_start: 0.7881 (mpp80) cc_final: 0.7552 (mtm-85) REVERT: LY 111 LEU cc_start: 0.6881 (mm) cc_final: 0.6525 (tt) REVERT: LY 117 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8202 (mtmm) outliers start: 24 outliers final: 19 residues processed: 171 average time/residue: 0.1180 time to fit residues: 29.2171 Evaluate side-chains 166 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 100 GLU Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain Lk residue 42 LEU Chi-restraints excluded: chain LR residue 145 LEU Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 79 VAL Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 117 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 20.0000 chunk 62 optimal weight: 0.0570 chunk 72 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN LR 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.196095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.157075 restraints weight = 29295.239| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 3.10 r_work: 0.3570 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15829 Z= 0.173 Angle : 0.625 7.941 22871 Z= 0.312 Chirality : 0.037 0.199 2814 Planarity : 0.004 0.044 1675 Dihedral : 23.524 169.552 6261 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.71 % Allowed : 15.87 % Favored : 80.42 % 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: -1.48 (0.25), residues: 961 helix: -0.44 (0.26), residues: 406 sheet: -0.95 (0.48), residues: 115 loop : -1.43 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGLR 16 TYR 0.017 0.001 TYRLY 74 PHE 0.011 0.002 PHELR 132 TRP 0.009 0.001 TRPLR 95 HIS 0.004 0.001 HISLR 75 Details of bonding type rmsd covalent geometry : bond 0.00360 (15829) covalent geometry : angle 0.62520 (22871) hydrogen bonds : bond 0.06377 ( 551) hydrogen bonds : angle 3.74433 ( 1282) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7913 (t) REVERT: A 163 ASN cc_start: 0.3585 (OUTLIER) cc_final: 0.2652 (m-40) REVERT: A 311 LYS cc_start: 0.7438 (mmtt) cc_final: 0.7156 (mmtp) REVERT: A 331 MET cc_start: 0.2027 (ttp) cc_final: 0.0189 (mtt) REVERT: LR 88 ARG cc_start: 0.8402 (mtp180) cc_final: 0.6457 (mmt180) REVERT: LX 50 LYS cc_start: 0.8438 (ptmt) cc_final: 0.7746 (tptp) REVERT: LX 69 ASN cc_start: 0.8153 (t0) cc_final: 0.7554 (t0) REVERT: LY 84 ARG cc_start: 0.7864 (mpp80) cc_final: 0.7524 (mtm-85) REVERT: LY 117 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8308 (mtmm) outliers start: 32 outliers final: 23 residues processed: 169 average time/residue: 0.1263 time to fit residues: 30.9717 Evaluate side-chains 170 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 100 GLU Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain Lk residue 42 LEU Chi-restraints excluded: chain LR residue 145 LEU Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 120 ASP Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 79 VAL Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 117 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS LR 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.198980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.166072 restraints weight = 29668.259| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.37 r_work: 0.3658 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15829 Z= 0.111 Angle : 0.566 8.688 22871 Z= 0.285 Chirality : 0.035 0.199 2814 Planarity : 0.004 0.042 1675 Dihedral : 23.456 172.794 6261 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.90 % Allowed : 16.69 % Favored : 80.42 % 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: -1.25 (0.26), residues: 961 helix: -0.13 (0.26), residues: 408 sheet: -0.93 (0.47), residues: 117 loop : -1.40 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGLR 16 TYR 0.015 0.001 TYRLY 74 PHE 0.009 0.001 PHE A 117 TRP 0.009 0.001 TRPLR 95 HIS 0.004 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00222 (15829) covalent geometry : angle 0.56569 (22871) hydrogen bonds : bond 0.05687 ( 551) hydrogen bonds : angle 3.56115 ( 1282) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 THR cc_start: 0.8109 (m) cc_final: 0.7886 (t) REVERT: A 117 PHE cc_start: 0.6371 (m-80) cc_final: 0.6125 (m-80) REVERT: A 163 ASN cc_start: 0.3708 (OUTLIER) cc_final: 0.2890 (m-40) REVERT: A 185 MET cc_start: 0.5907 (mtp) cc_final: 0.5499 (mtm) REVERT: A 311 LYS cc_start: 0.7521 (mmtt) cc_final: 0.7166 (mmtp) REVERT: A 331 MET cc_start: 0.1874 (ttp) cc_final: 0.0191 (mtt) REVERT: Lk 69 LEU cc_start: 0.7876 (mm) cc_final: 0.7553 (mt) REVERT: LR 88 ARG cc_start: 0.8177 (mtp180) cc_final: 0.6346 (mmt180) REVERT: LX 50 LYS cc_start: 0.8276 (ptmt) cc_final: 0.7701 (tptp) REVERT: LX 69 ASN cc_start: 0.8048 (t0) cc_final: 0.7398 (t0) REVERT: LY 84 ARG cc_start: 0.7674 (mpp80) cc_final: 0.7376 (mtm-85) REVERT: LY 111 LEU cc_start: 0.6942 (mm) cc_final: 0.6601 (tt) REVERT: LY 117 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8224 (mtmm) outliers start: 25 outliers final: 21 residues processed: 173 average time/residue: 0.1310 time to fit residues: 32.1541 Evaluate side-chains 172 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 100 GLU Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 13 LEU Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LR residue 145 LEU Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 79 VAL Chi-restraints excluded: chain LY residue 99 ILE Chi-restraints excluded: chain LY residue 117 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 0.2980 chunk 18 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 20.0000 chunk 19 optimal weight: 0.0370 chunk 101 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN Lh 20 GLN LR 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.197143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.159516 restraints weight = 29532.525| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.83 r_work: 0.3599 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15829 Z= 0.151 Angle : 0.596 8.490 22871 Z= 0.297 Chirality : 0.036 0.200 2814 Planarity : 0.004 0.042 1675 Dihedral : 23.417 169.644 6261 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.13 % Allowed : 16.34 % Favored : 80.53 % 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: -1.24 (0.26), residues: 961 helix: -0.12 (0.26), residues: 408 sheet: -0.88 (0.47), residues: 115 loop : -1.41 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGLR 16 TYR 0.016 0.001 TYR A 343 PHE 0.010 0.001 PHELR 132 TRP 0.007 0.001 TRPLR 95 HIS 0.004 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00316 (15829) covalent geometry : angle 0.59565 (22871) hydrogen bonds : bond 0.06025 ( 551) hydrogen bonds : angle 3.64894 ( 1282) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ARG cc_start: 0.5926 (mmp-170) cc_final: 0.5707 (mmp-170) REVERT: A 163 ASN cc_start: 0.3576 (OUTLIER) cc_final: 0.2687 (m-40) REVERT: A 185 MET cc_start: 0.6116 (mtp) cc_final: 0.5849 (mtm) REVERT: A 311 LYS cc_start: 0.7443 (mmtt) cc_final: 0.7123 (mmtp) REVERT: A 331 MET cc_start: 0.1753 (ttp) cc_final: 0.0095 (mtt) REVERT: LR 88 ARG cc_start: 0.8353 (mtp180) cc_final: 0.6401 (mmt180) REVERT: LX 50 LYS cc_start: 0.8408 (ptmt) cc_final: 0.7808 (tptm) REVERT: LX 69 ASN cc_start: 0.8112 (t0) cc_final: 0.7512 (t0) REVERT: LY 84 ARG cc_start: 0.7787 (mpp80) cc_final: 0.7492 (mtm-85) REVERT: LY 117 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8228 (mtmm) outliers start: 27 outliers final: 21 residues processed: 167 average time/residue: 0.1265 time to fit residues: 29.9205 Evaluate side-chains 170 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 100 GLU Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LR residue 134 ASN Chi-restraints excluded: chain LR residue 145 LEU Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 79 VAL Chi-restraints excluded: chain LY residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 94 optimal weight: 0.0770 chunk 44 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 108 optimal weight: 30.0000 chunk 121 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Lh 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.197733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.160442 restraints weight = 29403.691| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.87 r_work: 0.3601 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15829 Z= 0.132 Angle : 0.582 8.499 22871 Z= 0.292 Chirality : 0.036 0.201 2814 Planarity : 0.004 0.041 1675 Dihedral : 23.397 171.217 6261 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.55 % Allowed : 16.69 % Favored : 80.76 % 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: -1.16 (0.26), residues: 961 helix: -0.05 (0.26), residues: 408 sheet: -0.85 (0.48), residues: 115 loop : -1.38 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGLR 16 TYR 0.016 0.001 TYRLY 74 PHE 0.011 0.001 PHELR 132 TRP 0.006 0.001 TRPLR 95 HIS 0.004 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00276 (15829) covalent geometry : angle 0.58250 (22871) hydrogen bonds : bond 0.05836 ( 551) hydrogen bonds : angle 3.63150 ( 1282) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 ASN cc_start: 0.3506 (OUTLIER) cc_final: 0.2665 (m-40) REVERT: A 311 LYS cc_start: 0.7482 (mmtt) cc_final: 0.7172 (mmtp) REVERT: A 331 MET cc_start: 0.1932 (ttp) cc_final: 0.0092 (mtt) REVERT: LR 88 ARG cc_start: 0.8308 (mtp180) cc_final: 0.6408 (mmt180) REVERT: LX 50 LYS cc_start: 0.8347 (ptmt) cc_final: 0.7771 (tptm) REVERT: LX 69 ASN cc_start: 0.8061 (t0) cc_final: 0.7419 (t0) REVERT: LY 84 ARG cc_start: 0.7739 (mpp80) cc_final: 0.7446 (mtm-85) REVERT: LY 117 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8209 (mtmm) outliers start: 22 outliers final: 19 residues processed: 160 average time/residue: 0.1272 time to fit residues: 28.7957 Evaluate side-chains 168 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 100 GLU Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain LR residue 145 LEU Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 79 VAL Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 115 optimal weight: 30.0000 chunk 99 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 107 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS A 178 ASN Lh 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.197448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.159271 restraints weight = 29451.824| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.97 r_work: 0.3591 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15829 Z= 0.141 Angle : 0.585 8.437 22871 Z= 0.292 Chirality : 0.036 0.201 2814 Planarity : 0.004 0.042 1675 Dihedral : 23.372 174.017 6261 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.78 % Allowed : 16.57 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.26), residues: 961 helix: -0.01 (0.26), residues: 408 sheet: -0.85 (0.48), residues: 115 loop : -1.40 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGLR 16 TYR 0.016 0.001 TYRLY 74 PHE 0.009 0.001 PHE A 117 TRP 0.006 0.001 TRPLR 95 HIS 0.003 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00295 (15829) covalent geometry : angle 0.58528 (22871) hydrogen bonds : bond 0.05874 ( 551) hydrogen bonds : angle 3.62875 ( 1282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4314.23 seconds wall clock time: 74 minutes 22.93 seconds (4462.93 seconds total)