Starting phenix.real_space_refine on Fri Aug 7 00:33:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u9s_42040/08_2026/8u9s_42040.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u9s_42040/08_2026/8u9s_42040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u9s_42040/08_2026/8u9s_42040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u9s_42040/08_2026/8u9s_42040.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u9s_42040/08_2026/8u9s_42040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u9s_42040/08_2026/8u9s_42040.map" } resolution = 2.6 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= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2242 atoms to isotropic. 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 324 5.49 5 S 32 5.16 5 C 9232 2.51 5 N 2970 2.21 5 O 3730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16288 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3311 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "J" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3331 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "M" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "N" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Time building chain proxies: 2.90, per 1000 atoms: 0.18 Number of scatterers: 16288 At special positions: 0 Unit cell: (135.181, 149.411, 131.116, 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 324 15.00 O 3730 8.00 N 2970 7.00 C 9232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 42 " - pdb=" SG CYS M 107 " distance=2.04 Simple disulfide: pdb=" SG CYS M 171 " - pdb=" SG CYS M 245 " distance=2.03 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS N 171 " - pdb=" SG CYS N 245 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 480.2 milliseconds 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 22 sheets defined 48.0% alpha, 22.0% beta 162 base pairs and 282 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.779A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.308A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.629A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.688A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.883A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.512A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.350A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.730A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 4.326A pdb=" N THR M 102 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 211 through 214 removed outlier: 3.699A pdb=" N LYS M 214 " --> pdb=" O GLU M 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 211 through 214' Processing helix chain 'M' and resid 236 through 240 Processing helix chain 'N' and resid 98 through 102 removed outlier: 3.712A pdb=" N THR N 102 " --> pdb=" O SER N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 179 No H-bonds generated for 'chain 'N' and resid 177 through 179' Processing helix chain 'N' and resid 236 through 240 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.800A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.166A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.586A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.841A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.231A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 23 through 25 removed outlier: 3.879A pdb=" N ASP M 89 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.297A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP M 54 " --> pdb=" O LEU M 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.297A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR M 116 " --> pdb=" O GLN M 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.408A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.408A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR M 258 " --> pdb=" O ARG M 247 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N SER M 249 " --> pdb=" O LEU M 256 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU M 256 " --> pdb=" O SER M 249 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 25 removed outlier: 3.717A pdb=" N ASP N 89 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32 removed outlier: 4.266A pdb=" N GLU N 124 " --> pdb=" O MET N 30 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA N 32 " --> pdb=" O GLU N 124 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 removed outlier: 4.266A pdb=" N GLU N 124 " --> pdb=" O MET N 30 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA N 32 " --> pdb=" O GLU N 124 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR N 116 " --> pdb=" O GLN N 109 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain 'N' and resid 159 through 161 removed outlier: 6.612A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TRP N 185 " --> pdb=" O ILE N 197 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 159 through 161 removed outlier: 3.999A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 412 hydrogen bonds 824 hydrogen bond angles 0 basepair planarities 162 basepair parallelities 282 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3798 1.34 - 1.46: 4874 1.46 - 1.57: 7890 1.57 - 1.69: 646 1.69 - 1.81: 52 Bond restraints: 17260 Sorted by residual: bond pdb=" C1' DC I 39 " pdb=" N1 DC I 39 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.37e+01 bond pdb=" C1' DC J 4 " pdb=" N1 DC J 4 " ideal model delta sigma weight residual 1.468 1.545 -0.077 1.40e-02 5.10e+03 3.01e+01 bond pdb=" C1' DC I 91 " pdb=" N1 DC I 91 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.95e+01 bond pdb=" C1' DC I 131 " pdb=" N1 DC I 131 " ideal model delta sigma weight residual 1.468 1.543 -0.075 1.40e-02 5.10e+03 2.87e+01 bond pdb=" C1' DT I 59 " pdb=" N1 DT I 59 " ideal model delta sigma weight residual 1.468 1.541 -0.073 1.40e-02 5.10e+03 2.73e+01 ... (remaining 17255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 22747 1.55 - 3.09: 1712 3.09 - 4.64: 216 4.64 - 6.19: 29 6.19 - 7.74: 8 Bond angle restraints: 24712 Sorted by residual: angle pdb=" N3 DT I 7 " pdb=" C4 DT I 7 " pdb=" O4 DT I 7 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT J 138 " pdb=" C4 DT J 138 " pdb=" O4 DT J 138 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" O5' DC J 4 " pdb=" C5' DC J 4 " pdb=" C4' DC J 4 " ideal model delta sigma weight residual 109.40 112.84 -3.44 8.00e-01 1.56e+00 1.85e+01 angle pdb=" O4' DC J 5 " pdb=" C1' DC J 5 " pdb=" N1 DC J 5 " ideal model delta sigma weight residual 108.00 110.99 -2.99 7.00e-01 2.04e+00 1.83e+01 angle pdb=" N3 DT J 7 " pdb=" C4 DT J 7 " pdb=" O4 DT J 7 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 ... (remaining 24707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 8108 34.88 - 69.75: 1398 69.75 - 104.63: 38 104.63 - 139.50: 0 139.50 - 174.38: 2 Dihedral angle restraints: 9546 sinusoidal: 6000 harmonic: 3546 Sorted by residual: dihedral pdb=" C4' DT J 143 " pdb=" C3' DT J 143 " pdb=" O3' DT J 143 " pdb=" P DG J 144 " ideal model delta sinusoidal sigma weight residual 220.00 45.62 174.38 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT J 109 " pdb=" C3' DT J 109 " pdb=" O3' DT J 109 " pdb=" P DG J 110 " ideal model delta sinusoidal sigma weight residual 220.00 70.12 149.88 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CB GLU G 91 " pdb=" CG GLU G 91 " pdb=" CD GLU G 91 " pdb=" OE1 GLU G 91 " ideal model delta sinusoidal sigma weight residual 0.00 88.92 -88.92 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 9543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1582 0.033 - 0.066: 723 0.066 - 0.100: 144 0.100 - 0.133: 220 0.133 - 0.166: 115 Chirality restraints: 2784 Sorted by residual: chirality pdb=" C3' DC I 81 " pdb=" C4' DC I 81 " pdb=" O3' DC I 81 " pdb=" C2' DC I 81 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" C3' DA I 82 " pdb=" C4' DA I 82 " pdb=" O3' DA I 82 " pdb=" C2' DA I 82 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" C3' DC J 128 " pdb=" C4' DC J 128 " pdb=" O3' DC J 128 " pdb=" C2' DC J 128 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 2781 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA J 73 " 0.027 2.00e-02 2.50e+03 1.27e-02 4.46e+00 pdb=" N9 DA J 73 " -0.029 2.00e-02 2.50e+03 pdb=" C8 DA J 73 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA J 73 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA J 73 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA J 73 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA J 73 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA J 73 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA J 73 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DA J 73 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DA J 73 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 91 " -0.024 2.00e-02 2.50e+03 1.33e-02 3.99e+00 pdb=" N1 DC I 91 " 0.026 2.00e-02 2.50e+03 pdb=" C2 DC I 91 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DC I 91 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DC I 91 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC I 91 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 91 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 91 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DC I 91 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 39 " 0.023 2.00e-02 2.50e+03 1.27e-02 3.64e+00 pdb=" N1 DC I 39 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DC I 39 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DC I 39 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DC I 39 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 39 " 0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 39 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 39 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DC I 39 " 0.001 2.00e-02 2.50e+03 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1624 2.75 - 3.29: 13600 3.29 - 3.83: 30368 3.83 - 4.36: 37065 4.36 - 4.90: 55031 Nonbonded interactions: 137688 Sorted by model distance: nonbonded pdb=" OD2 ASP N 222 " pdb=" OG SER N 225 " model vdw 2.214 3.040 nonbonded pdb=" N GLU M 124 " pdb=" OE1 GLU M 124 " model vdw 2.229 3.120 nonbonded pdb=" OD2 ASP M 222 " pdb=" OG SER M 225 " model vdw 2.280 3.040 nonbonded pdb=" O GLU M 162 " pdb=" OG1 THR M 165 " model vdw 2.285 3.040 nonbonded pdb=" N GLU N 124 " pdb=" OE1 GLU N 124 " model vdw 2.285 3.120 ... (remaining 137683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.550 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 : 0.007 0.081 17264 Z= 0.589 Angle : 0.847 7.736 24720 Z= 0.698 Chirality : 0.055 0.166 2784 Planarity : 0.005 0.070 1996 Dihedral : 25.639 174.380 7262 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.19 % Allowed : 13.68 % Favored : 86.13 % 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: 2.19 (0.24), residues: 1198 helix: 2.68 (0.22), residues: 534 sheet: 1.27 (0.33), residues: 246 loop : -0.05 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 86 TYR 0.009 0.001 TYR N 68 PHE 0.007 0.001 PHE F 61 TRP 0.006 0.001 TRP N 259 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.59 (17260) covalent geometry : angle 0.84664 / 0.70 (24712) SS BOND : bond 0.00378 / 0.20 ( 4) SS BOND : angle 0.85658 / 0.38 ( 8) hydrogen bonds : bond 0.13791 / 9.06 ( 964) hydrogen bonds : angle 4.76345 / 3.40 ( 2405) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.460 Fit side-chains REVERT: C 24 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6744 (mm110) REVERT: G 41 GLU cc_start: 0.8190 (tt0) cc_final: 0.7887 (tt0) REVERT: G 92 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7878 (mt-10) REVERT: N 208 LYS cc_start: 0.8618 (ttpt) cc_final: 0.8394 (ttmm) outliers start: 2 outliers final: 1 residues processed: 192 average time/residue: 0.7401 time to fit residues: 153.1707 Evaluate side-chains 181 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain M residue 113 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN F 27 GLN F 93 GLN H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.183112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.142370 restraints weight = 16883.646| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.44 r_work: 0.3717 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17264 Z= 0.164 Angle : 0.628 7.173 24720 Z= 0.378 Chirality : 0.047 0.234 2784 Planarity : 0.004 0.034 1996 Dihedral : 28.480 178.457 4910 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.83 % Allowed : 13.49 % Favored : 84.68 % 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: 2.34 (0.24), residues: 1198 helix: 2.72 (0.22), residues: 548 sheet: 1.52 (0.34), residues: 238 loop : -0.04 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.013 0.001 TYR H 42 PHE 0.009 0.001 PHE F 61 TRP 0.008 0.001 TRP M 185 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (17260) covalent geometry : angle 0.62774 / 0.38 (24712) SS BOND : bond 0.00575 / 0.29 ( 4) SS BOND : angle 1.17860 / 0.53 ( 8) hydrogen bonds : bond 0.05418 / 3.61 ( 964) hydrogen bonds : angle 3.67359 / 2.66 ( 2405) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.378 Fit side-chains REVERT: E 73 GLU cc_start: 0.8147 (tt0) cc_final: 0.7856 (tt0) REVERT: G 41 GLU cc_start: 0.8480 (tt0) cc_final: 0.8177 (tt0) REVERT: H 84 ASN cc_start: 0.8707 (m110) cc_final: 0.8440 (m-40) REVERT: M 80 ARG cc_start: 0.8515 (mtm110) cc_final: 0.8174 (mtm110) REVERT: M 98 GLU cc_start: 0.6265 (mp0) cc_final: 0.5983 (mp0) REVERT: M 124 GLU cc_start: 0.7593 (pm20) cc_final: 0.7386 (pm20) REVERT: N 23 MET cc_start: 0.8964 (tpt) cc_final: 0.8673 (tpt) REVERT: N 36 GLU cc_start: 0.7936 (pm20) cc_final: 0.7528 (pm20) outliers start: 19 outliers final: 10 residues processed: 198 average time/residue: 0.7255 time to fit residues: 154.2356 Evaluate side-chains 186 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 46 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 95 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 119 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN E 113 HIS H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.182936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.142017 restraints weight = 17014.143| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.44 r_work: 0.3711 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17264 Z= 0.140 Angle : 0.580 6.539 24720 Z= 0.345 Chirality : 0.044 0.251 2784 Planarity : 0.004 0.034 1996 Dihedral : 29.181 177.364 4907 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.89 % Allowed : 13.29 % Favored : 83.82 % 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: 2.49 (0.24), residues: 1198 helix: 2.85 (0.22), residues: 548 sheet: 1.68 (0.34), residues: 238 loop : -0.06 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.011 0.001 TYR H 42 PHE 0.008 0.001 PHE A 67 TRP 0.008 0.001 TRP M 196 HIS 0.004 0.001 HIS N 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (17260) covalent geometry : angle 0.57988 / 0.34 (24712) SS BOND : bond 0.00548 / 0.28 ( 4) SS BOND : angle 1.07952 / 0.51 ( 8) hydrogen bonds : bond 0.04661 / 3.11 ( 964) hydrogen bonds : angle 3.34946 / 2.42 ( 2405) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.374 Fit side-chains REVERT: B 68 ASP cc_start: 0.8207 (m-30) cc_final: 0.7937 (m-30) REVERT: E 73 GLU cc_start: 0.8092 (tt0) cc_final: 0.7812 (tt0) REVERT: G 41 GLU cc_start: 0.8486 (tt0) cc_final: 0.8163 (tt0) REVERT: H 116 LYS cc_start: 0.8306 (tttp) cc_final: 0.7815 (ttpt) REVERT: M 80 ARG cc_start: 0.8486 (mtm110) cc_final: 0.8040 (mtm110) REVERT: M 98 GLU cc_start: 0.6340 (mp0) cc_final: 0.5853 (mp0) REVERT: M 124 GLU cc_start: 0.7624 (pm20) cc_final: 0.7274 (pm20) REVERT: M 152 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: M 165 THR cc_start: 0.7965 (p) cc_final: 0.7545 (t) REVERT: N 36 GLU cc_start: 0.7935 (pm20) cc_final: 0.7505 (pm20) REVERT: N 208 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8247 (ttpt) outliers start: 30 outliers final: 14 residues processed: 192 average time/residue: 0.7034 time to fit residues: 144.9052 Evaluate side-chains 186 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 152 GLN Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 208 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 50.0000 chunk 93 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS C 24 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 47 GLN G 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.181278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.140535 restraints weight = 16819.939| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.41 r_work: 0.3696 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17264 Z= 0.154 Angle : 0.588 6.514 24720 Z= 0.343 Chirality : 0.044 0.250 2784 Planarity : 0.004 0.030 1996 Dihedral : 29.330 175.940 4907 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.28 % Allowed : 13.58 % Favored : 83.14 % 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: 2.41 (0.24), residues: 1198 helix: 2.80 (0.22), residues: 548 sheet: 1.54 (0.34), residues: 240 loop : -0.06 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.016 0.001 TYR M 209 PHE 0.008 0.001 PHE F 61 TRP 0.008 0.001 TRP N 196 HIS 0.004 0.001 HIS N 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (17260) covalent geometry : angle 0.58798 / 0.34 (24712) SS BOND : bond 0.00654 / 0.34 ( 4) SS BOND : angle 1.31563 / 0.63 ( 8) hydrogen bonds : bond 0.04912 / 3.26 ( 964) hydrogen bonds : angle 3.28449 / 2.38 ( 2405) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.372 Fit side-chains REVERT: B 68 ASP cc_start: 0.8259 (m-30) cc_final: 0.7935 (m-30) REVERT: B 77 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7659 (mtpt) REVERT: C 90 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.7861 (t70) REVERT: E 73 GLU cc_start: 0.8209 (tt0) cc_final: 0.7831 (tt0) REVERT: G 41 GLU cc_start: 0.8443 (tt0) cc_final: 0.8091 (tt0) REVERT: H 42 TYR cc_start: 0.7793 (t80) cc_final: 0.7490 (t80) REVERT: M 80 ARG cc_start: 0.8453 (mtm110) cc_final: 0.8234 (mtm110) REVERT: M 98 GLU cc_start: 0.6262 (mp0) cc_final: 0.5672 (mp0) REVERT: M 124 GLU cc_start: 0.7658 (pm20) cc_final: 0.7278 (pm20) REVERT: M 192 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7848 (mt0) REVERT: M 200 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8617 (tp) REVERT: M 230 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.6585 (tpt) REVERT: N 36 GLU cc_start: 0.7921 (pm20) cc_final: 0.7427 (pm20) REVERT: N 195 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7695 (mt-10) REVERT: N 208 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8262 (ttpt) outliers start: 34 outliers final: 15 residues processed: 187 average time/residue: 0.7504 time to fit residues: 150.6210 Evaluate side-chains 192 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 192 GLN Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 99 SER Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain N residue 208 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 89 optimal weight: 50.0000 chunk 85 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.176983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.135827 restraints weight = 16720.553| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.40 r_work: 0.3638 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17264 Z= 0.244 Angle : 0.676 8.525 24720 Z= 0.381 Chirality : 0.050 0.270 2784 Planarity : 0.005 0.037 1996 Dihedral : 29.528 175.384 4907 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.66 % Allowed : 13.97 % Favored : 82.37 % 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: 1.88 (0.24), residues: 1198 helix: 2.35 (0.22), residues: 548 sheet: 1.31 (0.34), residues: 240 loop : -0.31 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 40 TYR 0.017 0.002 TYR H 42 PHE 0.011 0.002 PHE B 100 TRP 0.012 0.002 TRP M 259 HIS 0.006 0.001 HIS N 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 (17260) covalent geometry : angle 0.67540 / 0.38 (24712) SS BOND : bond 0.00961 / 0.49 ( 4) SS BOND : angle 2.20628 / 1.06 ( 8) hydrogen bonds : bond 0.06989 / 4.69 ( 964) hydrogen bonds : angle 3.45964 / 2.49 ( 2405) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.410 Fit side-chains REVERT: B 77 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7810 (mtpt) REVERT: C 51 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7676 (tp) REVERT: D 35 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: E 73 GLU cc_start: 0.8290 (tt0) cc_final: 0.7936 (tt0) REVERT: E 120 MET cc_start: 0.8140 (mtt) cc_final: 0.7885 (mtt) REVERT: G 41 GLU cc_start: 0.8446 (tt0) cc_final: 0.8111 (tt0) REVERT: G 91 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: H 42 TYR cc_start: 0.7922 (t80) cc_final: 0.7650 (t80) REVERT: H 76 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: M 80 ARG cc_start: 0.8437 (mtm110) cc_final: 0.8184 (mtm110) REVERT: M 98 GLU cc_start: 0.6337 (mp0) cc_final: 0.5705 (mp0) REVERT: M 124 GLU cc_start: 0.7717 (pm20) cc_final: 0.7295 (pm20) REVERT: M 200 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8581 (tp) REVERT: N 36 GLU cc_start: 0.7847 (pm20) cc_final: 0.7279 (pm20) REVERT: N 195 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: N 208 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8337 (ttpt) REVERT: N 230 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7163 (tpt) outliers start: 38 outliers final: 20 residues processed: 186 average time/residue: 0.7526 time to fit residues: 150.3807 Evaluate side-chains 196 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 99 SER Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 230 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 16 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.179253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.138131 restraints weight = 16672.861| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.41 r_work: 0.3665 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17264 Z= 0.151 Angle : 0.624 7.268 24720 Z= 0.355 Chirality : 0.046 0.255 2784 Planarity : 0.004 0.035 1996 Dihedral : 29.575 174.932 4907 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.47 % Allowed : 15.03 % Favored : 81.50 % 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: 2.00 (0.24), residues: 1198 helix: 2.51 (0.22), residues: 548 sheet: 1.28 (0.33), residues: 240 loop : -0.28 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.013 0.002 TYR H 42 PHE 0.008 0.001 PHE F 61 TRP 0.008 0.001 TRP M 196 HIS 0.004 0.001 HIS N 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (17260) covalent geometry : angle 0.62332 / 0.35 (24712) SS BOND : bond 0.00709 / 0.36 ( 4) SS BOND : angle 1.55834 / 0.75 ( 8) hydrogen bonds : bond 0.05200 / 3.47 ( 964) hydrogen bonds : angle 3.37631 / 2.44 ( 2405) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.309 Fit side-chains REVERT: B 77 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7803 (mtmt) REVERT: C 51 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7589 (tp) REVERT: D 35 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: E 73 GLU cc_start: 0.8203 (tt0) cc_final: 0.7865 (tt0) REVERT: E 120 MET cc_start: 0.7976 (mtt) cc_final: 0.7716 (mtt) REVERT: G 41 GLU cc_start: 0.8436 (tt0) cc_final: 0.8089 (tt0) REVERT: G 91 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: H 42 TYR cc_start: 0.7860 (t80) cc_final: 0.7622 (t80) REVERT: H 76 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: H 101 LEU cc_start: 0.8627 (mt) cc_final: 0.8414 (mt) REVERT: M 80 ARG cc_start: 0.8439 (mtm110) cc_final: 0.8155 (mtm110) REVERT: M 98 GLU cc_start: 0.6310 (mp0) cc_final: 0.5704 (mp0) REVERT: M 124 GLU cc_start: 0.7706 (pm20) cc_final: 0.7250 (pm20) REVERT: M 154 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7405 (mp10) REVERT: M 200 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8568 (tp) REVERT: N 36 GLU cc_start: 0.7863 (pm20) cc_final: 0.7269 (pm20) REVERT: N 195 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: N 208 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8295 (ttpt) outliers start: 36 outliers final: 18 residues processed: 182 average time/residue: 0.7722 time to fit residues: 151.1089 Evaluate side-chains 189 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 154 GLN Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain N residue 208 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 129 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.177619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.136459 restraints weight = 16690.538| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.40 r_work: 0.3646 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17264 Z= 0.230 Angle : 0.656 7.663 24720 Z= 0.371 Chirality : 0.048 0.270 2784 Planarity : 0.005 0.037 1996 Dihedral : 29.598 174.766 4907 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.99 % Allowed : 15.61 % Favored : 81.41 % 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: 1.81 (0.24), residues: 1198 helix: 2.34 (0.22), residues: 548 sheet: 1.22 (0.34), residues: 240 loop : -0.40 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 71 TYR 0.016 0.002 TYR H 42 PHE 0.010 0.002 PHE B 100 TRP 0.009 0.002 TRP M 196 HIS 0.005 0.001 HIS N 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (17260) covalent geometry : angle 0.65556 / 0.37 (24712) SS BOND : bond 0.00855 / 0.44 ( 4) SS BOND : angle 1.94454 / 0.93 ( 8) hydrogen bonds : bond 0.06159 / 4.11 ( 964) hydrogen bonds : angle 3.41378 / 2.46 ( 2405) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.377 Fit side-chains REVERT: A 120 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7939 (mmt) REVERT: B 77 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7836 (mtpt) REVERT: C 51 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7682 (tp) REVERT: C 73 ASN cc_start: 0.7814 (t160) cc_final: 0.7597 (t0) REVERT: D 35 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: E 73 GLU cc_start: 0.8237 (tt0) cc_final: 0.7876 (tt0) REVERT: E 120 MET cc_start: 0.8103 (mtt) cc_final: 0.7836 (mtt) REVERT: G 41 GLU cc_start: 0.8433 (tt0) cc_final: 0.8082 (tt0) REVERT: G 91 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: H 42 TYR cc_start: 0.7974 (t80) cc_final: 0.7728 (t80) REVERT: H 76 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: M 80 ARG cc_start: 0.8426 (mtm110) cc_final: 0.8125 (mtm110) REVERT: M 98 GLU cc_start: 0.6339 (mp0) cc_final: 0.5710 (mp0) REVERT: M 124 GLU cc_start: 0.7719 (pm20) cc_final: 0.7278 (pm20) REVERT: M 200 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8565 (tp) REVERT: N 36 GLU cc_start: 0.7853 (pm20) cc_final: 0.7602 (pm20) REVERT: N 208 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8320 (ttpt) REVERT: N 230 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7314 (tpt) outliers start: 31 outliers final: 18 residues processed: 175 average time/residue: 0.7979 time to fit residues: 149.7288 Evaluate side-chains 191 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 208 LYS Chi-restraints excluded: chain N residue 230 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 92 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 88 optimal weight: 50.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.166986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120395 restraints weight = 16707.725| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.51 r_work: 0.3405 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17264 Z= 0.204 Angle : 0.644 7.604 24720 Z= 0.364 Chirality : 0.047 0.266 2784 Planarity : 0.004 0.032 1996 Dihedral : 29.627 174.620 4907 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.47 % Allowed : 15.41 % Favored : 81.12 % 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: 1.81 (0.24), residues: 1198 helix: 2.38 (0.22), residues: 546 sheet: 1.18 (0.33), residues: 240 loop : -0.43 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.015 0.002 TYR H 42 PHE 0.009 0.002 PHE F 61 TRP 0.008 0.002 TRP M 196 HIS 0.005 0.001 HIS N 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (17260) covalent geometry : angle 0.64300 / 0.36 (24712) SS BOND : bond 0.00800 / 0.41 ( 4) SS BOND : angle 1.81334 / 0.87 ( 8) hydrogen bonds : bond 0.05731 / 3.81 ( 964) hydrogen bonds : angle 3.38695 / 2.45 ( 2405) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.307 Fit side-chains REVERT: A 120 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7831 (mmt) REVERT: B 77 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7704 (mtpt) REVERT: C 51 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7503 (tp) REVERT: D 35 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: E 73 GLU cc_start: 0.8104 (tt0) cc_final: 0.7724 (tt0) REVERT: G 41 GLU cc_start: 0.8392 (tt0) cc_final: 0.8013 (tt0) REVERT: H 42 TYR cc_start: 0.7844 (t80) cc_final: 0.7588 (t80) REVERT: H 76 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7642 (tm-30) REVERT: M 80 ARG cc_start: 0.8315 (mtm110) cc_final: 0.7966 (mtm110) REVERT: M 98 GLU cc_start: 0.6200 (mp0) cc_final: 0.5531 (mp0) REVERT: M 124 GLU cc_start: 0.7624 (pm20) cc_final: 0.7127 (pm20) REVERT: M 200 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8471 (tp) REVERT: N 36 GLU cc_start: 0.7768 (pm20) cc_final: 0.7500 (pm20) REVERT: N 208 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8207 (ttpt) outliers start: 36 outliers final: 21 residues processed: 180 average time/residue: 0.7969 time to fit residues: 153.7080 Evaluate side-chains 191 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 99 SER Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 208 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.168589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122052 restraints weight = 16727.665| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.52 r_work: 0.3426 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17264 Z= 0.140 Angle : 0.615 7.272 24720 Z= 0.352 Chirality : 0.046 0.254 2784 Planarity : 0.004 0.031 1996 Dihedral : 29.609 174.725 4907 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.79 % Allowed : 15.99 % Favored : 81.21 % 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: 2.00 (0.24), residues: 1198 helix: 2.59 (0.22), residues: 546 sheet: 1.18 (0.33), residues: 240 loop : -0.35 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 42 TYR 0.014 0.001 TYR H 42 PHE 0.008 0.001 PHE F 61 TRP 0.015 0.002 TRP N 185 HIS 0.003 0.001 HIS N 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (17260) covalent geometry : angle 0.61477 / 0.35 (24712) SS BOND : bond 0.00652 / 0.33 ( 4) SS BOND : angle 1.34632 / 0.65 ( 8) hydrogen bonds : bond 0.04867 / 3.24 ( 964) hydrogen bonds : angle 3.35187 / 2.43 ( 2405) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.298 Fit side-chains REVERT: B 77 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7658 (mtpt) REVERT: C 51 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7403 (tp) REVERT: D 35 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: E 73 GLU cc_start: 0.8061 (tt0) cc_final: 0.7678 (tt0) REVERT: E 120 MET cc_start: 0.7860 (mtt) cc_final: 0.7587 (mtt) REVERT: G 41 GLU cc_start: 0.8411 (tt0) cc_final: 0.8037 (tt0) REVERT: H 42 TYR cc_start: 0.7717 (t80) cc_final: 0.7453 (t80) REVERT: H 76 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: M 80 ARG cc_start: 0.8310 (mtm110) cc_final: 0.7958 (mtm110) REVERT: M 98 GLU cc_start: 0.6165 (mp0) cc_final: 0.5494 (mp0) REVERT: M 124 GLU cc_start: 0.7554 (pm20) cc_final: 0.7047 (pm20) REVERT: M 192 GLN cc_start: 0.8308 (mt0) cc_final: 0.7381 (mt0) REVERT: M 200 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8449 (tp) REVERT: N 36 GLU cc_start: 0.7813 (pm20) cc_final: 0.7568 (pm20) REVERT: N 208 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8176 (ttpt) outliers start: 29 outliers final: 21 residues processed: 170 average time/residue: 0.7793 time to fit residues: 142.1897 Evaluate side-chains 186 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 99 SER Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain N residue 208 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 17 optimal weight: 0.0470 chunk 107 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 108 optimal weight: 0.0770 chunk 141 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.169320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122846 restraints weight = 16718.965| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.52 r_work: 0.3436 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 17264 Z= 0.126 Angle : 0.604 6.810 24720 Z= 0.347 Chirality : 0.045 0.251 2784 Planarity : 0.004 0.030 1996 Dihedral : 29.607 174.527 4907 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.22 % Allowed : 16.67 % Favored : 81.12 % 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: 2.14 (0.24), residues: 1198 helix: 2.74 (0.22), residues: 546 sheet: 1.20 (0.33), residues: 240 loop : -0.30 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 71 TYR 0.012 0.001 TYR H 42 PHE 0.007 0.001 PHE A 67 TRP 0.017 0.001 TRP N 185 HIS 0.002 0.001 HIS N 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.13 (17260) covalent geometry : angle 0.60375 / 0.35 (24712) SS BOND : bond 0.00562 / 0.29 ( 4) SS BOND : angle 1.19019 / 0.56 ( 8) hydrogen bonds : bond 0.04555 / 3.02 ( 964) hydrogen bonds : angle 3.30221 / 2.40 ( 2405) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.365 Fit side-chains REVERT: B 77 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7644 (mtpt) REVERT: C 51 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7419 (tp) REVERT: D 35 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: E 73 GLU cc_start: 0.8052 (tt0) cc_final: 0.7522 (tt0) REVERT: E 120 MET cc_start: 0.7825 (mtt) cc_final: 0.7517 (mtt) REVERT: G 41 GLU cc_start: 0.8399 (tt0) cc_final: 0.8023 (tt0) REVERT: H 42 TYR cc_start: 0.7694 (t80) cc_final: 0.7430 (t80) REVERT: H 76 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: M 80 ARG cc_start: 0.8307 (mtm110) cc_final: 0.7949 (mtm110) REVERT: M 98 GLU cc_start: 0.6164 (mp0) cc_final: 0.5492 (mp0) REVERT: M 124 GLU cc_start: 0.7547 (pm20) cc_final: 0.7039 (pm20) REVERT: M 200 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8442 (tp) REVERT: N 36 GLU cc_start: 0.7804 (pm20) cc_final: 0.7557 (pm20) REVERT: N 208 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8156 (ttpt) outliers start: 23 outliers final: 17 residues processed: 165 average time/residue: 0.7862 time to fit residues: 138.9554 Evaluate side-chains 180 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 195 GLU Chi-restraints excluded: chain N residue 208 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 147 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 138 optimal weight: 0.0570 chunk 109 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.168729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.122205 restraints weight = 16658.975| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.52 r_work: 0.3429 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17264 Z= 0.157 Angle : 0.603 6.937 24720 Z= 0.346 Chirality : 0.045 0.260 2784 Planarity : 0.004 0.031 1996 Dihedral : 29.579 174.941 4907 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.41 % Allowed : 16.67 % Favored : 80.92 % 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: 2.09 (0.24), residues: 1198 helix: 2.71 (0.22), residues: 546 sheet: 1.16 (0.33), residues: 240 loop : -0.33 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 71 TYR 0.014 0.001 TYR H 42 PHE 0.008 0.001 PHE F 61 TRP 0.009 0.001 TRP M 185 HIS 0.004 0.001 HIS N 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (17260) covalent geometry : angle 0.60301 / 0.35 (24712) SS BOND : bond 0.00646 / 0.33 ( 4) SS BOND : angle 1.36163 / 0.65 ( 8) hydrogen bonds : bond 0.04888 / 3.24 ( 964) hydrogen bonds : angle 3.27276 / 2.37 ( 2405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6154.36 seconds wall clock time: 104 minutes 50.23 seconds (6290.23 seconds total)