Starting phenix.real_space_refine on Fri Oct 23 12:27:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36pf_77735/10_2026/36pf_77735.cif Found real_map, /net/cci-nas-00/data/ceres_data/36pf_77735/10_2026/36pf_77735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/36pf_77735/10_2026/36pf_77735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36pf_77735/10_2026/36pf_77735.map" model { file = "/net/cci-nas-00/data/ceres_data/36pf_77735/10_2026/36pf_77735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36pf_77735/10_2026/36pf_77735.cif" } resolution = 3.4 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= 0.013 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 98 5.49 5 S 65 5.16 5 C 5860 2.51 5 N 1682 2.21 5 O 2097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9802 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "E" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "F" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "H" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "A" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1357 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 10, 'rna3p_pur': 22, 'rna3p_pyr': 16} Link IDs: {'rna2p': 24, 'rna3p': 38} Chain: "C" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 244 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "B" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 481 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Time building chain proxies: 2.33, per 1000 atoms: 0.24 Number of scatterers: 9802 At special positions: 0 Unit cell: (90.06, 110.58, 132.24, 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 65 16.00 P 98 15.00 O 2097 8.00 N 1682 7.00 C 5860 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: 0.86 Conformation dependent library (CDL) restraints added in 337.0 milliseconds 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 15 sheets defined 42.2% alpha, 36.0% beta 18 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.623A pdb=" N ASP D 23 " --> pdb=" O THR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 42 through 57 removed outlier: 3.578A pdb=" N SER D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 82 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 86 through 93 removed outlier: 3.842A pdb=" N ASP D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 117 through 120 removed outlier: 6.749A pdb=" N ASP D 120 " --> pdb=" O LYS D 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 117 through 120' Processing helix chain 'D' and resid 158 through 173 Processing helix chain 'E' and resid 19 through 23 removed outlier: 3.701A pdb=" N ASP E 23 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 42 through 57 Processing helix chain 'E' and resid 70 through 82 removed outlier: 3.626A pdb=" N CYS E 76 " --> pdb=" O MET E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 86 through 93 removed outlier: 3.810A pdb=" N ASP E 91 " --> pdb=" O GLY E 87 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 117 through 120 removed outlier: 6.546A pdb=" N ASP E 120 " --> pdb=" O LYS E 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 120' Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'F' and resid 19 through 23 Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 42 through 58 removed outlier: 3.637A pdb=" N THR F 56 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS F 58 " --> pdb=" O LEU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 82 Processing helix chain 'F' and resid 83 through 85 No H-bonds generated for 'chain 'F' and resid 83 through 85' Processing helix chain 'F' and resid 86 through 93 removed outlier: 3.667A pdb=" N ASP F 91 " --> pdb=" O GLY F 87 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 116 Processing helix chain 'F' and resid 117 through 120 removed outlier: 6.129A pdb=" N ASP F 120 " --> pdb=" O LYS F 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 117 through 120' Processing helix chain 'F' and resid 158 through 173 Processing helix chain 'G' and resid 19 through 23 removed outlier: 3.598A pdb=" N ASP G 23 " --> pdb=" O THR G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.524A pdb=" N LEU G 35 " --> pdb=" O TYR G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 58 removed outlier: 3.686A pdb=" N LEU G 48 " --> pdb=" O GLU G 44 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 82 Processing helix chain 'G' and resid 83 through 85 No H-bonds generated for 'chain 'G' and resid 83 through 85' Processing helix chain 'G' and resid 86 through 93 removed outlier: 3.781A pdb=" N ARG G 92 " --> pdb=" O LYS G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 116 Processing helix chain 'G' and resid 158 through 173 removed outlier: 3.955A pdb=" N MET G 164 " --> pdb=" O GLU G 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 23 removed outlier: 3.752A pdb=" N ASP H 23 " --> pdb=" O THR H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 37 Processing helix chain 'H' and resid 42 through 58 removed outlier: 3.748A pdb=" N CYS H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.789A pdb=" N LYS H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 93 removed outlier: 4.152A pdb=" N ARG H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 Processing helix chain 'H' and resid 117 through 120 removed outlier: 6.194A pdb=" N ASP H 120 " --> pdb=" O LYS H 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 117 through 120' Processing helix chain 'H' and resid 158 through 173 Processing sheet with id=AA1, first strand: chain 'D' and resid 60 through 61 removed outlier: 5.282A pdb=" N PHE D 66 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N VAL D 100 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N GLY D 149 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU D 147 " --> pdb=" O PRO D 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 60 through 61 removed outlier: 5.282A pdb=" N PHE D 66 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N VAL D 100 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N GLY D 149 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU D 147 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N TRP D 144 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 3 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU D 192 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN D 5 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 14 through 15 Processing sheet with id=AA4, first strand: chain 'E' and resid 60 through 61 removed outlier: 5.162A pdb=" N PHE E 66 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N VAL E 100 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N GLY E 149 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU E 147 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 60 through 61 removed outlier: 5.162A pdb=" N PHE E 66 " --> pdb=" O MET E 103 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N VAL E 100 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N GLY E 149 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU E 147 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TRP E 144 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU E 3 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU E 192 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASN E 5 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AA7, first strand: chain 'F' and resid 60 through 61 removed outlier: 5.305A pdb=" N PHE F 66 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N VAL F 100 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N GLY F 149 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU F 147 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 60 through 61 removed outlier: 5.305A pdb=" N PHE F 66 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N VAL F 100 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N GLY F 149 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU F 147 " --> pdb=" O PRO F 102 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TRP F 144 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER F 191 " --> pdb=" O ASN F 5 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS F 7 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE F 189 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR F 9 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL F 187 " --> pdb=" O THR F 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 14 through 15 Processing sheet with id=AB1, first strand: chain 'G' and resid 60 through 61 removed outlier: 5.283A pdb=" N PHE G 66 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N VAL G 100 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N GLY G 149 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU G 147 " --> pdb=" O PRO G 102 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TRP G 144 " --> pdb=" O GLY G 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 94 through 96 removed outlier: 5.182A pdb=" N TRP G 144 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU G 3 " --> pdb=" O GLU G 192 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU G 192 " --> pdb=" O LEU G 3 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN G 5 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 14 through 15 Processing sheet with id=AB4, first strand: chain 'H' and resid 60 through 61 removed outlier: 5.131A pdb=" N PHE H 66 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N VAL H 100 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLY H 149 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU H 147 " --> pdb=" O PRO H 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 60 through 61 removed outlier: 5.131A pdb=" N PHE H 66 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N VAL H 100 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLY H 149 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU H 147 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TRP H 144 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU H 3 " --> pdb=" O GLU H 192 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU H 192 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN H 5 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 14 through 15 422 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2473 1.33 - 1.45: 2237 1.45 - 1.57: 5180 1.57 - 1.69: 193 1.69 - 1.81: 110 Bond restraints: 10193 Sorted by residual: bond pdb=" C3' DG B 34 " pdb=" C2' DG B 34 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.37e+01 bond pdb=" C3' DA B 26 " pdb=" C2' DA B 26 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DA C 36 " pdb=" C2' DA C 36 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DT B 37 " pdb=" C2' DT B 37 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.14e+00 bond pdb=" C3' DC C 28 " pdb=" C2' DC C 28 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.55e+00 ... (remaining 10188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 13604 1.31 - 2.62: 473 2.62 - 3.93: 116 3.93 - 5.23: 10 5.23 - 6.54: 4 Bond angle restraints: 14207 Sorted by residual: angle pdb=" O4' DG C 32 " pdb=" C1' DG C 32 " pdb=" N9 DG C 32 " ideal model delta sigma weight residual 108.00 114.54 -6.54 7.00e-01 2.04e+00 8.73e+01 angle pdb=" C4' DG C 32 " pdb=" O4' DG C 32 " pdb=" C1' DG C 32 " ideal model delta sigma weight residual 110.10 103.83 6.27 1.00e+00 1.00e+00 3.93e+01 angle pdb=" C3' G A 78 " pdb=" O3' G A 78 " pdb=" P U A 79 " ideal model delta sigma weight residual 119.70 125.36 -5.66 1.20e+00 6.94e-01 2.23e+01 angle pdb=" C2' U A 57 " pdb=" C1' U A 57 " pdb=" N1 U A 57 " ideal model delta sigma weight residual 112.00 117.00 -5.00 1.10e+00 8.26e-01 2.07e+01 angle pdb=" C3' U A 57 " pdb=" O3' U A 57 " pdb=" P G A 58 " ideal model delta sigma weight residual 119.70 125.06 -5.36 1.20e+00 6.94e-01 2.00e+01 ... (remaining 14202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 5900 35.53 - 71.06: 273 71.06 - 106.59: 23 106.59 - 142.12: 1 142.12 - 177.65: 4 Dihedral angle restraints: 6201 sinusoidal: 3371 harmonic: 2830 Sorted by residual: dihedral pdb=" O4' U A 30 " pdb=" C1' U A 30 " pdb=" N1 U A 30 " pdb=" C2 U A 30 " ideal model delta sinusoidal sigma weight residual -128.00 46.90 -174.90 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U A 55 " pdb=" C1' U A 55 " pdb=" N1 U A 55 " pdb=" C2 U A 55 " ideal model delta sinusoidal sigma weight residual 232.00 67.12 164.88 1 1.70e+01 3.46e-03 6.53e+01 dihedral pdb=" O4' U A 80 " pdb=" C1' U A 80 " pdb=" N1 U A 80 " pdb=" C2 U A 80 " ideal model delta sinusoidal sigma weight residual -160.00 -94.27 -65.73 1 1.50e+01 4.44e-03 2.51e+01 ... (remaining 6198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1212 0.049 - 0.099: 318 0.099 - 0.148: 98 0.148 - 0.197: 9 0.197 - 0.247: 3 Chirality restraints: 1640 Sorted by residual: chirality pdb=" C1' A A 37 " pdb=" O4' A A 37 " pdb=" C2' A A 37 " pdb=" N9 A A 37 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C1' DG C 32 " pdb=" O4' DG C 32 " pdb=" C2' DG C 32 " pdb=" N9 DG C 32 " both_signs ideal model delta sigma weight residual False 2.43 2.21 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C3' DA B 22 " pdb=" C4' DA B 22 " pdb=" O3' DA B 22 " pdb=" C2' DA B 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1637 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG C 32 " -0.041 2.00e-02 2.50e+03 1.86e-02 1.04e+01 pdb=" N9 DG C 32 " 0.048 2.00e-02 2.50e+03 pdb=" C8 DG C 32 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG C 32 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG C 32 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG C 32 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG C 32 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG C 32 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG C 32 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG C 32 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG C 32 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG C 32 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 57 " 0.036 2.00e-02 2.50e+03 1.88e-02 7.95e+00 pdb=" N1 U A 57 " -0.041 2.00e-02 2.50e+03 pdb=" C2 U A 57 " -0.007 2.00e-02 2.50e+03 pdb=" O2 U A 57 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U A 57 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U A 57 " 0.005 2.00e-02 2.50e+03 pdb=" O4 U A 57 " 0.011 2.00e-02 2.50e+03 pdb=" C5 U A 57 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U A 57 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 37 " 0.032 2.00e-02 2.50e+03 1.42e-02 5.58e+00 pdb=" N9 A A 37 " -0.032 2.00e-02 2.50e+03 pdb=" C8 A A 37 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A A 37 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A A 37 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A A 37 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A A 37 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A A 37 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A A 37 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A A 37 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A A 37 " -0.003 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 4517 2.99 - 3.47: 8965 3.47 - 3.94: 15661 3.94 - 4.42: 18059 4.42 - 4.90: 28873 Nonbonded interactions: 76075 Sorted by model distance: nonbonded pdb=" O5' DC C 37 " pdb=" O4' DC C 37 " model vdw 2.510 2.432 nonbonded pdb=" O5' DT C 38 " pdb=" O4' DT C 38 " model vdw 2.515 2.432 nonbonded pdb=" CE1 HIS D 17 " pdb=" O6 G A 58 " model vdw 2.558 3.260 nonbonded pdb=" O2' U A 80 " pdb=" O4' A A 81 " model vdw 2.585 3.040 nonbonded pdb=" N1 G A 31 " pdb=" C4 G A 31 " model vdw 2.586 2.672 ... (remaining 76070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 3.670 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.810 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10193 Z= 0.249 Angle : 0.596 6.542 14207 Z= 0.480 Chirality : 0.049 0.247 1640 Planarity : 0.004 0.033 1448 Dihedral : 18.122 177.655 4371 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.70 (0.26), residues: 965 helix: 1.03 (0.28), residues: 340 sheet: 0.73 (0.33), residues: 230 loop : -0.06 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 133 TYR 0.012 0.001 TYR E 59 PHE 0.010 0.001 PHE G 14 TRP 0.004 0.001 TRP D 178 HIS 0.003 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.25 (10193) covalent geometry : angle 0.59615 / 0.48 (14207) hydrogen bonds : bond 0.17977 / 12.35 ( 432) hydrogen bonds : angle 7.54503 / 5.25 ( 1267) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.318 Fit side-chains REVERT: E 68 MET cc_start: 0.7948 (ttm) cc_final: 0.7733 (ttm) REVERT: E 190 MET cc_start: 0.6536 (mmp) cc_final: 0.6255 (mmm) REVERT: G 177 ASP cc_start: 0.7724 (t0) cc_final: 0.7450 (t0) REVERT: H 135 MET cc_start: 0.8375 (tpt) cc_final: 0.8150 (mmt) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1009 time to fit residues: 29.0469 Evaluate side-chains 126 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 38, 61] chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN D 107 ASN F 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.160110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.124211 restraints weight = 12516.071| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.23 r_work: 0.3322 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10193 Z= 0.149 Angle : 0.573 7.825 14207 Z= 0.328 Chirality : 0.047 0.452 1640 Planarity : 0.004 0.033 1448 Dihedral : 22.196 179.196 2416 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.63 % Allowed : 7.79 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.89 (0.26), residues: 965 helix: 1.22 (0.27), residues: 370 sheet: 0.87 (0.32), residues: 230 loop : -0.13 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 92 TYR 0.021 0.002 TYR H 31 PHE 0.022 0.002 PHE H 152 TRP 0.004 0.001 TRP H 144 HIS 0.004 0.001 HIS D 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (10193) covalent geometry : angle 0.57286 / 0.33 (14207) hydrogen bonds : bond 0.04497 / 3.02 ( 432) hydrogen bonds : angle 5.62123 / 3.87 ( 1267) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.317 Fit side-chains REVERT: D 1 MET cc_start: 0.8322 (mmt) cc_final: 0.8088 (mmm) REVERT: D 151 MET cc_start: 0.7914 (mtp) cc_final: 0.7545 (mtm) REVERT: E 45 ASP cc_start: 0.8015 (m-30) cc_final: 0.7793 (m-30) REVERT: E 95 MET cc_start: 0.7776 (ptp) cc_final: 0.7498 (ptt) REVERT: G 119 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8505 (tp40) REVERT: G 131 THR cc_start: 0.8898 (p) cc_final: 0.8537 (t) REVERT: G 177 ASP cc_start: 0.7948 (t0) cc_final: 0.7635 (t0) REVERT: H 153 ASP cc_start: 0.5667 (t0) cc_final: 0.5330 (t0) outliers start: 14 outliers final: 6 residues processed: 144 average time/residue: 0.0768 time to fit residues: 16.5998 Evaluate side-chains 124 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain G residue 29 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [33, 44, 67, 76, 43, 17, 42, 19, 15, 93, 45] chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.159583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123353 restraints weight = 12531.267| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.24 r_work: 0.3321 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10193 Z= 0.144 Angle : 0.553 7.111 14207 Z= 0.314 Chirality : 0.046 0.445 1640 Planarity : 0.004 0.033 1448 Dihedral : 22.227 179.116 2416 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.51 % Allowed : 10.35 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.96 (0.26), residues: 965 helix: 1.42 (0.28), residues: 370 sheet: 0.71 (0.32), residues: 230 loop : -0.12 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 133 TYR 0.014 0.001 TYR E 59 PHE 0.013 0.002 PHE D 14 TRP 0.004 0.001 TRP G 144 HIS 0.004 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (10193) covalent geometry : angle 0.55304 / 0.31 (14207) hydrogen bonds : bond 0.03835 / 2.57 ( 432) hydrogen bonds : angle 5.16872 / 3.55 ( 1267) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.300 Fit side-chains REVERT: D 151 MET cc_start: 0.7897 (mtp) cc_final: 0.7480 (mtm) REVERT: D 163 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8380 (mm) REVERT: E 45 ASP cc_start: 0.7930 (m-30) cc_final: 0.7728 (m-30) REVERT: E 95 MET cc_start: 0.7720 (ptp) cc_final: 0.7434 (ptt) REVERT: G 119 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8596 (tp40) REVERT: G 131 THR cc_start: 0.8920 (p) cc_final: 0.8551 (t) REVERT: G 177 ASP cc_start: 0.7915 (t0) cc_final: 0.7600 (t0) REVERT: H 72 MET cc_start: 0.7575 (ttm) cc_final: 0.7282 (ttm) REVERT: H 107 ASN cc_start: 0.7839 (t0) cc_final: 0.7590 (t0) REVERT: H 153 ASP cc_start: 0.5463 (t0) cc_final: 0.5261 (t0) outliers start: 13 outliers final: 7 residues processed: 130 average time/residue: 0.0725 time to fit residues: 14.2933 Evaluate side-chains 127 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain H residue 158 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [26, 22, 35, 15, 55, 45, 74, 60, 97, 75, 86] chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.154740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117743 restraints weight = 12700.983| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.33 r_work: 0.3247 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10193 Z= 0.251 Angle : 0.637 8.031 14207 Z= 0.353 Chirality : 0.051 0.477 1640 Planarity : 0.005 0.036 1448 Dihedral : 22.427 179.956 2416 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.86 % Allowed : 12.56 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.52 (0.26), residues: 965 helix: 1.24 (0.28), residues: 370 sheet: 0.25 (0.32), residues: 230 loop : -0.41 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 133 TYR 0.018 0.002 TYR F 59 PHE 0.023 0.003 PHE D 14 TRP 0.009 0.001 TRP G 144 HIS 0.007 0.002 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 (10193) covalent geometry : angle 0.63702 / 0.35 (14207) hydrogen bonds : bond 0.04483 / 3.01 ( 432) hydrogen bonds : angle 5.14345 / 3.54 ( 1267) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: D 151 MET cc_start: 0.8030 (mtp) cc_final: 0.7657 (mtm) REVERT: D 163 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8419 (mm) REVERT: E 45 ASP cc_start: 0.8102 (m-30) cc_final: 0.7876 (m-30) REVERT: E 95 MET cc_start: 0.7744 (ptp) cc_final: 0.7439 (ptt) REVERT: G 131 THR cc_start: 0.8943 (p) cc_final: 0.8600 (t) REVERT: H 107 ASN cc_start: 0.8019 (t0) cc_final: 0.7709 (t0) outliers start: 16 outliers final: 11 residues processed: 140 average time/residue: 0.0863 time to fit residues: 17.6189 Evaluate side-chains 132 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 158 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [98, 58, 38, 97, 78, 80, 96, 40, 65, 50, 10] chunk 98 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.153746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.117609 restraints weight = 12501.644| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.26 r_work: 0.3238 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10193 Z= 0.266 Angle : 0.655 8.184 14207 Z= 0.362 Chirality : 0.051 0.482 1640 Planarity : 0.005 0.040 1448 Dihedral : 22.616 179.971 2416 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.79 % Allowed : 14.07 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.14 (0.26), residues: 965 helix: 1.08 (0.28), residues: 370 sheet: -0.11 (0.32), residues: 230 loop : -0.68 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 133 TYR 0.023 0.002 TYR H 60 PHE 0.023 0.003 PHE D 14 TRP 0.008 0.001 TRP G 144 HIS 0.008 0.002 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.27 (10193) covalent geometry : angle 0.65526 / 0.36 (14207) hydrogen bonds : bond 0.04510 / 3.06 ( 432) hydrogen bonds : angle 5.13964 / 3.55 ( 1267) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.312 Fit side-chains REVERT: D 151 MET cc_start: 0.8061 (mtp) cc_final: 0.7714 (mtm) REVERT: D 163 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8406 (mm) REVERT: E 45 ASP cc_start: 0.8011 (m-30) cc_final: 0.7808 (m-30) REVERT: E 95 MET cc_start: 0.7703 (ptp) cc_final: 0.7407 (ptt) REVERT: G 23 ASP cc_start: 0.7743 (t70) cc_final: 0.7240 (p0) REVERT: G 131 THR cc_start: 0.8928 (p) cc_final: 0.8627 (t) REVERT: H 92 ARG cc_start: 0.7579 (ptt-90) cc_final: 0.7357 (mtp180) REVERT: H 107 ASN cc_start: 0.7993 (t0) cc_final: 0.7587 (t0) REVERT: H 153 ASP cc_start: 0.6426 (t0) cc_final: 0.6161 (t0) outliers start: 24 outliers final: 19 residues processed: 139 average time/residue: 0.0813 time to fit residues: 16.8433 Evaluate side-chains 142 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 158 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [45, 63, 74, 94, 97, 40, 91, 5, 82, 16, 20] chunk 45 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 0.0050 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.157376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121347 restraints weight = 12497.795| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.27 r_work: 0.3298 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10193 Z= 0.129 Angle : 0.534 8.481 14207 Z= 0.302 Chirality : 0.045 0.432 1640 Planarity : 0.004 0.039 1448 Dihedral : 22.521 178.201 2416 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.86 % Allowed : 15.70 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.51 (0.26), residues: 965 helix: 1.48 (0.28), residues: 370 sheet: -0.10 (0.32), residues: 240 loop : -0.47 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 133 TYR 0.012 0.001 TYR E 59 PHE 0.013 0.001 PHE H 152 TRP 0.006 0.001 TRP H 144 HIS 0.002 0.001 HIS D 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (10193) covalent geometry : angle 0.53389 / 0.30 (14207) hydrogen bonds : bond 0.03370 / 2.29 ( 432) hydrogen bonds : angle 4.81293 / 3.31 ( 1267) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.257 Fit side-chains REVERT: D 151 MET cc_start: 0.8101 (mtp) cc_final: 0.7706 (mtm) REVERT: E 95 MET cc_start: 0.7615 (ptp) cc_final: 0.7311 (ptt) REVERT: F 19 ASP cc_start: 0.8837 (p0) cc_final: 0.8592 (p0) REVERT: G 131 THR cc_start: 0.8801 (p) cc_final: 0.8463 (t) REVERT: H 68 MET cc_start: 0.7771 (ttp) cc_final: 0.7555 (ttp) REVERT: H 107 ASN cc_start: 0.7986 (t0) cc_final: 0.7612 (t0) outliers start: 16 outliers final: 12 residues processed: 135 average time/residue: 0.0815 time to fit residues: 16.4044 Evaluate side-chains 127 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [92, 94, 71, 96, 0, 75, 56, 66, 79, 85, 7] chunk 92 optimal weight: 4.9990 chunk 94 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 79 optimal weight: 0.0670 chunk 85 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.158519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122443 restraints weight = 12432.634| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.24 r_work: 0.3324 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10193 Z= 0.114 Angle : 0.517 8.426 14207 Z= 0.291 Chirality : 0.044 0.420 1640 Planarity : 0.004 0.061 1448 Dihedral : 22.445 177.916 2416 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.33 % Allowed : 15.35 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.76 (0.27), residues: 965 helix: 1.70 (0.28), residues: 370 sheet: 0.00 (0.32), residues: 240 loop : -0.31 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 92 TYR 0.014 0.001 TYR H 31 PHE 0.010 0.001 PHE H 14 TRP 0.003 0.000 TRP H 144 HIS 0.002 0.001 HIS D 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (10193) covalent geometry : angle 0.51733 / 0.29 (14207) hydrogen bonds : bond 0.03164 / 2.12 ( 432) hydrogen bonds : angle 4.66117 / 3.20 ( 1267) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.251 Fit side-chains REVERT: D 151 MET cc_start: 0.8105 (mtp) cc_final: 0.7726 (mtm) REVERT: D 163 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8317 (mm) REVERT: E 95 MET cc_start: 0.7544 (ptp) cc_final: 0.7250 (ptt) REVERT: F 19 ASP cc_start: 0.8782 (p0) cc_final: 0.8569 (p0) REVERT: G 131 THR cc_start: 0.8715 (p) cc_final: 0.8351 (t) REVERT: H 9 THR cc_start: 0.8438 (m) cc_final: 0.8205 (p) REVERT: H 107 ASN cc_start: 0.7987 (t0) cc_final: 0.7649 (t0) outliers start: 20 outliers final: 18 residues processed: 132 average time/residue: 0.0722 time to fit residues: 14.3759 Evaluate side-chains 132 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [37, 14, 58, 20, 1, 24, 86, 42, 45, 95, 93] chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.158109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.122592 restraints weight = 12531.469| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.23 r_work: 0.3312 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10193 Z= 0.129 Angle : 0.526 10.582 14207 Z= 0.293 Chirality : 0.044 0.422 1640 Planarity : 0.004 0.050 1448 Dihedral : 22.408 177.978 2416 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.33 % Allowed : 15.58 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.79 (0.27), residues: 965 helix: 1.74 (0.28), residues: 370 sheet: 0.01 (0.32), residues: 240 loop : -0.32 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 142 TYR 0.018 0.001 TYR H 60 PHE 0.012 0.001 PHE D 14 TRP 0.004 0.001 TRP G 144 HIS 0.003 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (10193) covalent geometry : angle 0.52582 / 0.29 (14207) hydrogen bonds : bond 0.03201 / 2.14 ( 432) hydrogen bonds : angle 4.58923 / 3.15 ( 1267) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.327 Fit side-chains REVERT: D 151 MET cc_start: 0.8106 (mtp) cc_final: 0.7737 (mtm) REVERT: D 163 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8348 (mm) REVERT: E 95 MET cc_start: 0.7584 (ptp) cc_final: 0.7265 (ptt) REVERT: F 19 ASP cc_start: 0.8919 (p0) cc_final: 0.8682 (p0) REVERT: G 131 THR cc_start: 0.8725 (p) cc_final: 0.8370 (t) REVERT: H 9 THR cc_start: 0.8515 (m) cc_final: 0.8291 (p) REVERT: H 107 ASN cc_start: 0.8003 (t0) cc_final: 0.7654 (t0) outliers start: 20 outliers final: 17 residues processed: 133 average time/residue: 0.0703 time to fit residues: 14.2093 Evaluate side-chains 135 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [53, 28, 38, 8, 34, 0, 17, 35, 62, 93, 42] chunk 53 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.158325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.122926 restraints weight = 12473.692| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.23 r_work: 0.3314 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10193 Z= 0.127 Angle : 0.525 9.512 14207 Z= 0.294 Chirality : 0.044 0.416 1640 Planarity : 0.005 0.059 1448 Dihedral : 22.416 177.689 2416 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.44 % Allowed : 15.93 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.81 (0.27), residues: 965 helix: 1.76 (0.28), residues: 370 sheet: 0.02 (0.32), residues: 240 loop : -0.30 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 133 TYR 0.016 0.001 TYR H 31 PHE 0.011 0.001 PHE D 14 TRP 0.003 0.001 TRP H 144 HIS 0.003 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (10193) covalent geometry : angle 0.52489 / 0.29 (14207) hydrogen bonds : bond 0.03200 / 2.15 ( 432) hydrogen bonds : angle 4.55298 / 3.13 ( 1267) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.318 Fit side-chains REVERT: D 151 MET cc_start: 0.8108 (mtp) cc_final: 0.7747 (mtm) REVERT: D 163 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8337 (mm) REVERT: E 95 MET cc_start: 0.7549 (ptp) cc_final: 0.7233 (ptt) REVERT: F 19 ASP cc_start: 0.8914 (p0) cc_final: 0.8680 (p0) REVERT: G 131 THR cc_start: 0.8670 (p) cc_final: 0.8311 (t) REVERT: G 153 ASP cc_start: 0.7194 (t70) cc_final: 0.6674 (t0) REVERT: H 9 THR cc_start: 0.8492 (m) cc_final: 0.8273 (p) REVERT: H 107 ASN cc_start: 0.8001 (t0) cc_final: 0.7641 (t0) outliers start: 21 outliers final: 18 residues processed: 133 average time/residue: 0.0714 time to fit residues: 14.5374 Evaluate side-chains 135 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [97, 78, 12, 11, 19, 45, 55, 25, 59, 43, 33] chunk 97 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.0370 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.1864 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.156830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.121415 restraints weight = 12365.597| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.23 r_work: 0.3294 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10193 Z= 0.167 Angle : 0.559 9.767 14207 Z= 0.311 Chirality : 0.045 0.424 1640 Planarity : 0.005 0.048 1448 Dihedral : 22.453 177.962 2416 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.09 % Allowed : 16.63 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.70 (0.27), residues: 965 helix: 1.72 (0.28), residues: 370 sheet: -0.06 (0.32), residues: 240 loop : -0.41 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 179 TYR 0.016 0.001 TYR H 31 PHE 0.015 0.002 PHE D 14 TRP 0.005 0.001 TRP G 144 HIS 0.005 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (10193) covalent geometry : angle 0.55944 / 0.31 (14207) hydrogen bonds : bond 0.03495 / 2.35 ( 432) hydrogen bonds : angle 4.60559 / 3.16 ( 1267) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.328 Fit side-chains REVERT: D 151 MET cc_start: 0.8159 (mtp) cc_final: 0.7804 (mtm) REVERT: D 163 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8396 (mm) REVERT: E 95 MET cc_start: 0.7584 (ptp) cc_final: 0.7263 (ptt) REVERT: E 190 MET cc_start: 0.7598 (mmm) cc_final: 0.7246 (mmm) REVERT: F 19 ASP cc_start: 0.8943 (p0) cc_final: 0.8702 (p0) REVERT: G 131 THR cc_start: 0.8760 (p) cc_final: 0.8405 (t) REVERT: G 153 ASP cc_start: 0.7056 (t70) cc_final: 0.6700 (t0) REVERT: G 194 ASN cc_start: 0.6229 (m-40) cc_final: 0.5919 (m-40) REVERT: H 9 THR cc_start: 0.8506 (m) cc_final: 0.8258 (p) REVERT: H 60 TYR cc_start: 0.7146 (t80) cc_final: 0.6735 (t80) REVERT: H 107 ASN cc_start: 0.8022 (t0) cc_final: 0.7670 (t0) outliers start: 18 outliers final: 16 residues processed: 131 average time/residue: 0.0776 time to fit residues: 15.3983 Evaluate side-chains 135 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: [60, 65, 81, 93, 95, 54, 82, 67, 14, 45, 19] chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.153383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117076 restraints weight = 12556.352| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.27 r_work: 0.3254 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10193 Z= 0.247 Angle : 0.646 9.201 14207 Z= 0.353 Chirality : 0.049 0.448 1640 Planarity : 0.005 0.050 1448 Dihedral : 22.597 178.667 2416 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.56 % Allowed : 16.16 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.32 (0.27), residues: 965 helix: 1.39 (0.28), residues: 370 sheet: -0.34 (0.31), residues: 260 loop : -0.53 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 179 TYR 0.020 0.002 TYR F 59 PHE 0.023 0.003 PHE D 14 TRP 0.009 0.002 TRP G 144 HIS 0.008 0.002 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.25 (10193) covalent geometry : angle 0.64592 / 0.35 (14207) hydrogen bonds : bond 0.04374 / 2.97 ( 432) hydrogen bonds : angle 4.88601 / 3.37 ( 1267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2261.21 seconds wall clock time: 39 minutes 34.39 seconds (2374.39 seconds total)