Starting phenix.real_space_refine on Sat Sep 12 09:35:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6sxo_10344/09_2026/6sxo_10344.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sxo_10344/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6sxo_10344/09_2026/6sxo_10344.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6sxo_10344/09_2026/6sxo_10344.cif" model { file = "/net/cci-nas-00/data/ceres_data/6sxo_10344/09_2026/6sxo_10344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sxo_10344/09_2026/6sxo_10344.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sxo_10344/09_2026/6sxo_10344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sxo_10344/09_2026/6sxo_10344.map" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: 2.54, per 1000 atoms: 0.17 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: 0.81 Conformation dependent library (CDL) restraints added in 396.5 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: 1.82 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: 2.93 Time building geometry restraints manager: 1.23 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 1.478 1.558 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" O3' UL53583 " pdb=" P CL53584 " ideal model delta sigma weight residual 1.607 1.639 -0.032 1.20e-02 6.94e+03 7.04e+00 bond pdb=" O3' GL53256 " pdb=" P GL53257 " ideal model delta sigma weight residual 1.607 1.637 -0.030 1.20e-02 6.94e+03 6.08e+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 ... (remaining 15824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 21701 3.18 - 6.35: 1036 6.35 - 9.53: 108 9.53 - 12.71: 18 12.71 - 15.88: 8 Bond angle restraints: 22871 Sorted by residual: angle pdb=" C3' UL53583 " pdb=" O3' UL53583 " pdb=" P CL53584 " ideal model delta sigma weight residual 119.70 131.51 -11.81 1.20e+00 6.94e-01 9.68e+01 angle pdb=" C3' GL53256 " pdb=" O3' GL53256 " pdb=" P GL53257 " ideal model delta sigma weight residual 119.70 130.53 -10.83 1.20e+00 6.94e-01 8.15e+01 angle pdb=" C3' GL53283 " pdb=" O3' GL53283 " pdb=" P CL53284 " ideal model delta sigma weight residual 119.70 129.72 -10.02 1.20e+00 6.94e-01 6.98e+01 angle pdb=" C3' UL53578 " pdb=" O3' UL53578 " pdb=" P CL53579 " ideal model delta sigma weight residual 119.70 129.53 -9.83 1.20e+00 6.94e-01 6.72e+01 angle pdb=" O3' CL53294 " pdb=" P GL53295 " pdb=" O5' GL53295 " ideal model delta sigma weight residual 104.00 119.07 -15.07 1.90e+00 2.77e-01 6.29e+01 ... (remaining 22866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 8268 34.71 - 69.42: 684 69.42 - 104.12: 41 104.12 - 138.83: 2 138.83 - 173.54: 3 Dihedral angle restraints: 8998 sinusoidal: 6145 harmonic: 2853 Sorted by residual: dihedral pdb=" C4' AL52695 " pdb=" C3' AL52695 " pdb=" C2' AL52695 " pdb=" C1' AL52695 " ideal model delta sinusoidal sigma weight residual 36.35 -41.79 78.14 1 3.10e+00 1.04e-01 7.94e+02 dihedral pdb=" C4' UL52519 " pdb=" C3' UL52519 " pdb=" C2' UL52519 " pdb=" C1' UL52519 " ideal model delta sinusoidal sigma weight residual 36.35 -41.16 77.50 1 3.10e+00 1.04e-01 7.83e+02 dihedral pdb=" C4' CL8 83 " pdb=" C3' CL8 83 " pdb=" C2' CL8 83 " pdb=" C1' CL8 83 " ideal model delta sinusoidal sigma weight residual 36.34 -39.89 76.23 1 3.10e+00 1.04e-01 7.61e+02 ... (remaining 8995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 2319 0.139 - 0.277: 397 0.277 - 0.416: 83 0.416 - 0.555: 14 0.555 - 0.694: 1 Chirality restraints: 2814 Sorted by residual: chirality pdb=" P GL53580 " pdb=" OP1 GL53580 " pdb=" OP2 GL53580 " pdb=" O5' GL53580 " both_signs ideal model delta sigma weight residual True 2.17 -2.87 -0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" C4' CL52943 " pdb=" C5' CL52943 " pdb=" O4' CL52943 " pdb=" C3' CL52943 " both_signs ideal model delta sigma weight residual False -2.49 -1.94 -0.55 2.00e-01 2.50e+01 7.55e+00 chirality pdb=" P CL53296 " pdb=" OP1 CL53296 " pdb=" OP2 CL53296 " pdb=" O5' CL53296 " both_signs ideal model delta sigma weight residual True 2.17 -2.70 -0.53 2.00e-01 2.50e+01 6.94e+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: 11.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.720 Find NCS groups from input model: 0.050 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 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= 0.416 Angle : 1.495 15.883 22871 Z= 0.672 Chirality : 0.114 0.694 2814 Planarity : 0.007 0.058 1675 Dihedral : 19.297 173.540 7138 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/Z covalent geometry : bond 0.00893 / 0.42 (15829) covalent geometry : angle 1.49478 / 0.67 (22871) hydrogen bonds : bond 0.20558 / 13.86 ( 551) hydrogen bonds : angle 7.26496 / 4.99 ( 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 : 0.353 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: 0.1534 time to fit residues: 52.8039 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 : 0.389 ------------------------------------------------------------------------------- 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: 20.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0030 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 86 ASN LR 130 ASN LR 143 HIS LX 73 HIS LX 108 GLN LY 4 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.200886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.164100 restraints weight = 29715.432| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.92 r_work: 0.3652 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15829 Z= 0.200 Angle : 1.261 26.291 22871 Z= 0.509 Chirality : 0.103 1.759 2814 Planarity : 0.005 0.041 1675 Dihedral : 19.333 153.444 4971 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.01 % Allowed : 9.50 % Favored : 87.49 % 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: -2.88 (0.23), residues: 961 helix: -2.02 (0.22), residues: 406 sheet: -1.02 (0.46), residues: 115 loop : -1.94 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGLh 7 TYR 0.016 0.001 TYRLY 74 PHE 0.011 0.001 PHELR 132 TRP 0.010 0.002 TRPLR 95 HIS 0.008 0.001 HISLR 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 (15829) covalent geometry : angle 1.26068 / 0.51 (22871) hydrogen bonds : bond 0.08195 / 5.34 ( 551) hydrogen bonds : angle 4.34319 / 3.02 ( 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 220 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.7384 (pttt) cc_final: 0.7145 (tppt) REVERT: A 163 ASN cc_start: 0.4110 (p0) cc_final: 0.3830 (m-40) REVERT: A 238 LYS cc_start: 0.6312 (OUTLIER) cc_final: 0.6034 (tppt) REVERT: A 326 MET cc_start: 0.4814 (mmm) cc_final: 0.4048 (mmm) REVERT: Lh 22 ASP cc_start: 0.7675 (p0) cc_final: 0.7319 (p0) REVERT: LR 27 ASN cc_start: 0.8289 (m-40) cc_final: 0.8076 (m-40) REVERT: LR 34 ASN cc_start: 0.7899 (p0) cc_final: 0.7613 (p0) REVERT: LR 88 ARG cc_start: 0.8447 (mtp180) cc_final: 0.6510 (mmp-170) REVERT: LR 89 MET cc_start: 0.8148 (tpp) cc_final: 0.7707 (tpt) REVERT: LR 96 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7524 (ttt) REVERT: LX 50 LYS cc_start: 0.8248 (ptmt) cc_final: 0.7725 (tptp) REVERT: LX 69 ASN cc_start: 0.7872 (t0) cc_final: 0.7209 (t0) REVERT: LX 131 ASP cc_start: 0.7457 (t0) cc_final: 0.6903 (t0) outliers start: 26 outliers final: 16 residues processed: 208 average time/residue: 0.1272 time to fit residues: 37.9524 Evaluate side-chains 174 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 238 LYS Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 333 ILE 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 97 VAL 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 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 75 optimal weight: 0.0970 chunk 78 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 48 optimal weight: 0.0980 chunk 99 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 20 GLN LR 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.199090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.162439 restraints weight = 30126.263| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.87 r_work: 0.3635 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2836 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= 0.201 Angle : 1.091 16.277 22871 Z= 0.448 Chirality : 0.089 1.225 2814 Planarity : 0.005 0.044 1675 Dihedral : 19.244 159.832 4971 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.71 % Allowed : 12.28 % Favored : 84.01 % 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: -2.21 (0.24), residues: 961 helix: -1.37 (0.24), residues: 401 sheet: -0.99 (0.47), residues: 115 loop : -1.58 (0.25), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGLR 16 TYR 0.018 0.002 TYRLY 74 PHE 0.010 0.002 PHE A 283 TRP 0.013 0.002 TRPLR 95 HIS 0.006 0.002 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (15829) covalent geometry : angle 1.09057 / 0.45 (22871) hydrogen bonds : bond 0.07613 / 4.89 ( 551) hydrogen bonds : angle 3.99974 / 2.78 ( 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 192 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.7313 (pttt) cc_final: 0.7101 (tppt) REVERT: A 238 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.6229 (tppt) REVERT: A 311 LYS cc_start: 0.7299 (mmtt) cc_final: 0.7028 (mmtp) REVERT: A 320 LYS cc_start: 0.6875 (ttmt) cc_final: 0.6661 (mttt) REVERT: A 343 TYR cc_start: 0.5565 (m-80) cc_final: 0.5258 (m-80) REVERT: LR 27 ASN cc_start: 0.8417 (m-40) cc_final: 0.8168 (m-40) REVERT: LR 34 ASN cc_start: 0.7999 (p0) cc_final: 0.7753 (p0) REVERT: LR 88 ARG cc_start: 0.8302 (mtp180) cc_final: 0.6334 (mmp-170) REVERT: LR 96 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7854 (ttt) REVERT: LX 50 LYS cc_start: 0.8332 (ptmt) cc_final: 0.7725 (tptp) REVERT: LX 69 ASN cc_start: 0.7973 (t0) cc_final: 0.7335 (t0) REVERT: LX 133 GLU cc_start: 0.8589 (mp0) cc_final: 0.8151 (mp0) REVERT: LY 84 ARG cc_start: 0.7800 (mpp80) cc_final: 0.7576 (mtm-85) REVERT: LY 120 GLU cc_start: 0.7646 (pt0) cc_final: 0.7386 (pt0) outliers start: 32 outliers final: 20 residues processed: 178 average time/residue: 0.1178 time to fit residues: 30.7265 Evaluate side-chains 168 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 238 LYS Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 333 ILE 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 97 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 0.0870 chunk 96 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 chunk 121 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Lh 20 GLN LR 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.204344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.170844 restraints weight = 30462.702| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.69 r_work: 0.3733 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15829 Z= 0.138 Angle : 0.964 14.160 22871 Z= 0.392 Chirality : 0.076 0.938 2814 Planarity : 0.004 0.042 1675 Dihedral : 18.885 167.343 4970 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.43 % Allowed : 14.95 % Favored : 82.62 % 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: -1.72 (0.25), residues: 961 helix: -0.83 (0.25), residues: 412 sheet: -0.90 (0.47), residues: 117 loop : -1.40 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGLR 16 TYR 0.014 0.001 TYRLY 74 PHE 0.008 0.001 PHE A 177 TRP 0.009 0.001 TRPLR 95 HIS 0.005 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (15829) covalent geometry : angle 0.96360 / 0.39 (22871) hydrogen bonds : bond 0.06778 / 4.30 ( 551) hydrogen bonds : angle 3.57085 / 2.49 ( 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 203 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Lh 87 LYS cc_start: 0.5510 (mmmt) cc_final: 0.5277 (mtmm) REVERT: LR 27 ASN cc_start: 0.8262 (m-40) cc_final: 0.8013 (m-40) REVERT: LR 34 ASN cc_start: 0.7967 (p0) cc_final: 0.7737 (p0) REVERT: LR 88 ARG cc_start: 0.8189 (mtp180) cc_final: 0.6414 (mmt-90) REVERT: LR 146 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8250 (ttmt) REVERT: LX 50 LYS cc_start: 0.8148 (ptmt) cc_final: 0.7606 (tptp) REVERT: LX 69 ASN cc_start: 0.7933 (t0) cc_final: 0.7268 (t0) REVERT: LX 133 GLU cc_start: 0.8493 (mp0) cc_final: 0.8184 (mp0) REVERT: LY 42 TYR cc_start: 0.8193 (m-80) cc_final: 0.7965 (m-80) REVERT: LY 111 LEU cc_start: 0.6852 (mm) cc_final: 0.6287 (tt) REVERT: LY 120 GLU cc_start: 0.7572 (pt0) cc_final: 0.7287 (pt0) outliers start: 21 outliers final: 12 residues processed: 191 average time/residue: 0.1276 time to fit residues: 34.7526 Evaluate side-chains 166 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 239 ASP Chi-restraints excluded: chain A residue 333 ILE 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 LX residue 51 THR Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 94 optimal weight: 0.0270 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 37 optimal weight: 0.0050 chunk 62 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN LR 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.201809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.164510 restraints weight = 30249.434| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.80 r_work: 0.3684 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15829 Z= 0.159 Angle : 0.963 13.815 22871 Z= 0.392 Chirality : 0.077 0.852 2814 Planarity : 0.004 0.044 1675 Dihedral : 18.699 162.583 4969 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.90 % Allowed : 15.87 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.25), residues: 961 helix: -0.47 (0.26), residues: 405 sheet: -0.95 (0.47), residues: 117 loop : -1.37 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGLY 26 TYR 0.015 0.001 TYRLY 74 PHE 0.015 0.001 PHE A 177 TRP 0.010 0.001 TRPLR 95 HIS 0.007 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (15829) covalent geometry : angle 0.96301 / 0.39 (22871) hydrogen bonds : bond 0.06722 / 4.26 ( 551) hydrogen bonds : angle 3.60717 / 2.51 ( 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: 25 poor density : 162 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.4826 (pm20) cc_final: 0.3708 (pm20) REVERT: A 78 THR cc_start: 0.8127 (m) cc_final: 0.7805 (t) REVERT: A 320 LYS cc_start: 0.6862 (mttt) cc_final: 0.5988 (mttp) REVERT: LR 27 ASN cc_start: 0.8315 (m-40) cc_final: 0.8054 (m-40) REVERT: LR 34 ASN cc_start: 0.7935 (p0) cc_final: 0.7731 (p0) REVERT: LR 88 ARG cc_start: 0.8233 (mtp180) cc_final: 0.6440 (mmt-90) REVERT: LX 50 LYS cc_start: 0.8154 (ptmt) cc_final: 0.7659 (tptp) REVERT: LX 69 ASN cc_start: 0.8100 (t0) cc_final: 0.7474 (t0) outliers start: 25 outliers final: 20 residues processed: 174 average time/residue: 0.1198 time to fit residues: 30.3969 Evaluate side-chains 171 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 A residue 333 ILE 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 LX residue 45 THR Chi-restraints excluded: chain LX residue 51 THR Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LY residue 40 GLN Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 99 ILE Chi-restraints excluded: chain LY residue 111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 70 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 41 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN Lh 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.202937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.165607 restraints weight = 30130.849| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.70 r_work: 0.3709 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3920 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= 0.139 Angle : 0.934 14.171 22871 Z= 0.380 Chirality : 0.074 0.799 2814 Planarity : 0.004 0.043 1675 Dihedral : 18.592 163.136 4969 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.24 % Allowed : 16.11 % 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: -1.28 (0.25), residues: 961 helix: -0.29 (0.26), residues: 412 sheet: -0.83 (0.47), residues: 117 loop : -1.32 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGLY 84 TYR 0.014 0.001 TYRLY 74 PHE 0.010 0.001 PHE A 315 TRP 0.008 0.001 TRPLR 95 HIS 0.004 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (15829) covalent geometry : angle 0.93354 / 0.38 (22871) hydrogen bonds : bond 0.06449 / 4.09 ( 551) hydrogen bonds : angle 3.51431 / 2.45 ( 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 185 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 THR cc_start: 0.8037 (m) cc_final: 0.7739 (t) REVERT: A 320 LYS cc_start: 0.6771 (mttt) cc_final: 0.5952 (mttp) REVERT: LR 27 ASN cc_start: 0.8233 (m-40) cc_final: 0.7975 (m-40) REVERT: LR 88 ARG cc_start: 0.8178 (mtp180) cc_final: 0.6429 (mmt-90) REVERT: LX 50 LYS cc_start: 0.8119 (ptmt) cc_final: 0.7652 (tptp) REVERT: LX 69 ASN cc_start: 0.8045 (t0) cc_final: 0.7424 (t0) REVERT: LX 138 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8699 (p) REVERT: LY 42 TYR cc_start: 0.8235 (m-80) cc_final: 0.8011 (m-80) REVERT: LY 111 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6344 (tt) outliers start: 28 outliers final: 19 residues processed: 171 average time/residue: 0.1263 time to fit residues: 31.0667 Evaluate side-chains 171 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 A residue 333 ILE Chi-restraints excluded: chain Lh residue 18 LEU Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 36 VAL 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 133 GLU Chi-restraints excluded: chain LX residue 138 VAL Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 40 GLN Chi-restraints excluded: chain LY residue 99 ILE Chi-restraints excluded: chain LY residue 111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 70 optimal weight: 0.0370 chunk 34 optimal weight: 7.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.203012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.165252 restraints weight = 30111.264| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.81 r_work: 0.3703 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4097 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= 0.137 Angle : 0.922 13.725 22871 Z= 0.374 Chirality : 0.073 0.760 2814 Planarity : 0.004 0.041 1675 Dihedral : 18.491 163.789 4969 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.48 % Allowed : 16.22 % Favored : 80.30 % 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: -1.06 (0.26), residues: 961 helix: 0.02 (0.26), residues: 406 sheet: -0.79 (0.47), residues: 117 loop : -1.31 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGLY 84 TYR 0.013 0.001 TYRLY 74 PHE 0.009 0.001 PHELR 132 TRP 0.007 0.001 TRPLR 95 HIS 0.005 0.001 HISLR 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (15829) covalent geometry : angle 0.92188 / 0.37 (22871) hydrogen bonds : bond 0.06390 / 4.05 ( 551) hydrogen bonds : angle 3.45476 / 2.41 ( 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 186 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.5016 (pm20) cc_final: 0.3703 (pm20) REVERT: A 78 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7804 (t) REVERT: LR 27 ASN cc_start: 0.8273 (m-40) cc_final: 0.8048 (m-40) REVERT: LR 88 ARG cc_start: 0.8166 (mtp180) cc_final: 0.6416 (mmt-90) REVERT: LX 50 LYS cc_start: 0.8100 (ptmt) cc_final: 0.7652 (tptp) REVERT: LX 69 ASN cc_start: 0.7978 (t0) cc_final: 0.7333 (t0) REVERT: LY 111 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6378 (tt) outliers start: 30 outliers final: 18 residues processed: 171 average time/residue: 0.1190 time to fit residues: 29.8772 Evaluate side-chains 168 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 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 333 ILE Chi-restraints excluded: chain Lh residue 27 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 83 THR Chi-restraints excluded: chain LX residue 95 THR 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 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 75 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN Lh 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.203512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.168002 restraints weight = 30258.536| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.74 r_work: 0.3715 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15829 Z= 0.134 Angle : 0.915 13.715 22871 Z= 0.372 Chirality : 0.072 0.726 2814 Planarity : 0.004 0.040 1675 Dihedral : 18.413 164.126 4969 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.36 % Allowed : 16.22 % 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: -1.03 (0.26), residues: 961 helix: 0.07 (0.26), residues: 420 sheet: -0.75 (0.48), residues: 117 loop : -1.37 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGLY 84 TYR 0.013 0.001 TYRLY 74 PHE 0.008 0.001 PHELR 132 TRP 0.012 0.001 TRPLR 95 HIS 0.003 0.001 HISLR 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (15829) covalent geometry : angle 0.91544 / 0.37 (22871) hydrogen bonds : bond 0.06324 / 4.01 ( 551) hydrogen bonds : angle 3.42929 / 2.40 ( 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: 29 poor density : 154 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.4802 (pm20) cc_final: 0.3641 (pm20) REVERT: A 78 THR cc_start: 0.8004 (OUTLIER) cc_final: 0.7763 (t) REVERT: Lk 26 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.6611 (tttt) REVERT: Lk 69 LEU cc_start: 0.7987 (mm) cc_final: 0.7714 (mt) REVERT: LR 27 ASN cc_start: 0.8223 (m-40) cc_final: 0.8023 (m-40) REVERT: LR 88 ARG cc_start: 0.8203 (mtp180) cc_final: 0.6430 (mmt-90) REVERT: LX 50 LYS cc_start: 0.8146 (ptmt) cc_final: 0.7635 (tptp) REVERT: LX 69 ASN cc_start: 0.8012 (t0) cc_final: 0.7386 (t0) REVERT: LY 111 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6417 (tt) outliers start: 29 outliers final: 21 residues processed: 167 average time/residue: 0.1305 time to fit residues: 31.2955 Evaluate side-chains 173 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 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 291 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 26 LYS 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 LX residue 133 GLU 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 111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 HIS Lh 20 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 = 0.4472 r_free = 0.4472 target = 0.202976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.165833 restraints weight = 30322.949| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.71 r_work: 0.3705 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15829 Z= 0.139 Angle : 0.916 13.785 22871 Z= 0.371 Chirality : 0.072 0.681 2814 Planarity : 0.004 0.041 1675 Dihedral : 18.368 164.468 4969 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.13 % Allowed : 16.45 % 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: -0.90 (0.26), residues: 961 helix: 0.20 (0.26), residues: 414 sheet: -0.74 (0.49), residues: 117 loop : -1.30 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGLY 84 TYR 0.014 0.001 TYR A 343 PHE 0.011 0.001 PHE A 177 TRP 0.007 0.001 TRPLR 95 HIS 0.005 0.001 HISLR 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (15829) covalent geometry : angle 0.91552 / 0.37 (22871) hydrogen bonds : bond 0.06340 / 4.02 ( 551) hydrogen bonds : angle 3.40514 / 2.38 ( 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 180 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7801 (t) REVERT: A 318 GLN cc_start: 0.7548 (tt0) cc_final: 0.7328 (tt0) REVERT: Lk 26 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6655 (tttt) REVERT: Lk 69 LEU cc_start: 0.7985 (mm) cc_final: 0.7716 (mt) REVERT: LR 88 ARG cc_start: 0.8224 (mtp180) cc_final: 0.6462 (mmt-90) REVERT: LX 50 LYS cc_start: 0.8087 (ptmt) cc_final: 0.7651 (tptp) REVERT: LX 69 ASN cc_start: 0.7982 (t0) cc_final: 0.7375 (t0) outliers start: 27 outliers final: 22 residues processed: 165 average time/residue: 0.1285 time to fit residues: 30.3033 Evaluate side-chains 170 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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 A residue 333 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 26 LYS Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain Lk residue 42 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 84 GLU Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 97 VAL Chi-restraints excluded: chain LX residue 133 GLU Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 99 ILE Chi-restraints excluded: chain LY residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 121 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Lh 20 GLN LX 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.201336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.163132 restraints weight = 29992.566| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.61 r_work: 0.3680 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4400 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= 0.160 Angle : 0.944 13.534 22871 Z= 0.384 Chirality : 0.074 0.665 2814 Planarity : 0.004 0.041 1675 Dihedral : 18.395 164.271 4969 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.59 % Allowed : 16.45 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.26), residues: 961 helix: 0.17 (0.26), residues: 414 sheet: -0.75 (0.49), residues: 115 loop : -1.32 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGLR 16 TYR 0.016 0.001 TYRLY 74 PHE 0.008 0.001 PHELR 132 TRP 0.008 0.001 TRPLR 95 HIS 0.005 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (15829) covalent geometry : angle 0.94365 / 0.38 (22871) hydrogen bonds : bond 0.06411 / 4.11 ( 551) hydrogen bonds : angle 3.49371 / 2.44 ( 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 185 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.5141 (pm20) cc_final: 0.3736 (pm20) REVERT: LR 88 ARG cc_start: 0.8318 (mtp180) cc_final: 0.6483 (mmt180) REVERT: LX 50 LYS cc_start: 0.8150 (ptmt) cc_final: 0.7725 (tptp) REVERT: LX 69 ASN cc_start: 0.7994 (t0) cc_final: 0.7398 (t0) outliers start: 31 outliers final: 25 residues processed: 170 average time/residue: 0.1252 time to fit residues: 30.7515 Evaluate side-chains 174 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 323 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 65 GLN Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Lk residue 26 LYS 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 84 GLU Chi-restraints excluded: chain LX residue 95 THR Chi-restraints excluded: chain LX residue 97 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 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 HIS Lh 20 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 = 0.4447 r_free = 0.4447 target = 0.200758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.163871 restraints weight = 30054.110| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.77 r_work: 0.3668 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15829 Z= 0.166 Angle : 0.953 13.566 22871 Z= 0.388 Chirality : 0.075 0.726 2814 Planarity : 0.004 0.041 1675 Dihedral : 18.417 164.324 4969 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.24 % Allowed : 16.92 % Favored : 79.84 % 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: -1.01 (0.26), residues: 961 helix: 0.09 (0.26), residues: 417 sheet: -0.74 (0.50), residues: 115 loop : -1.35 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGLY 84 TYR 0.016 0.001 TYRLY 74 PHE 0.010 0.001 PHE A 177 TRP 0.010 0.001 TRPLR 95 HIS 0.005 0.001 HISLh 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (15829) covalent geometry : angle 0.95324 / 0.39 (22871) hydrogen bonds : bond 0.06475 / 4.14 ( 551) hydrogen bonds : angle 3.52344 / 2.47 ( 1282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4274.10 seconds wall clock time: 73 minutes 54.64 seconds (4434.64 seconds total)