Starting phenix.real_space_refine on Thu Feb 5 14:41:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u9s_42040/02_2026/8u9s_42040.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u9s_42040/02_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_42040/02_2026/8u9s_42040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u9s_42040/02_2026/8u9s_42040.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u9s_42040/02_2026/8u9s_42040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u9s_42040/02_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-2.0-5952/lib/python3.9/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: 3.76, per 1000 atoms: 0.23 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: 1.48 Conformation dependent library (CDL) restraints added in 508.7 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: 2.53 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: 3.06 Time building geometry restraints manager: 1.95 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 1.490 1.549 -0.059 3.00e-02 1.11e+03 3.91e+00 bond pdb=" C3' DT J 143 " pdb=" O3' DT J 143 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.65e+00 bond pdb=" C1' DC J 4 " pdb=" N1 DC J 4 " ideal model delta sigma weight residual 1.490 1.545 -0.055 3.00e-02 1.11e+03 3.34e+00 bond pdb=" C1' DC I 91 " pdb=" N1 DC I 91 " ideal model delta sigma weight residual 1.490 1.544 -0.054 3.00e-02 1.11e+03 3.24e+00 bond pdb=" C LEU G 108 " pdb=" N PRO G 109 " ideal model delta sigma weight residual 1.333 1.351 -0.018 1.01e-02 9.80e+03 3.14e+00 ... (remaining 17255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 23468 1.55 - 3.09: 1077 3.09 - 4.64: 131 4.64 - 6.19: 28 6.19 - 7.74: 8 Bond angle restraints: 24712 Sorted by residual: angle pdb=" CA GLU M 238 " pdb=" CB GLU M 238 " pdb=" CG GLU M 238 " ideal model delta sigma weight residual 114.10 121.84 -7.74 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CB LYS B 77 " pdb=" CG LYS B 77 " pdb=" CD LYS B 77 " ideal model delta sigma weight residual 111.30 118.37 -7.07 2.30e+00 1.89e-01 9.45e+00 angle pdb=" C2' DC I 29 " pdb=" C1' DC I 29 " pdb=" N1 DC I 29 " ideal model delta sigma weight residual 113.50 118.11 -4.61 1.50e+00 4.44e-01 9.44e+00 angle pdb=" C2' DC I 39 " pdb=" C1' DC I 39 " pdb=" N1 DC I 39 " ideal model delta sigma weight residual 113.50 118.04 -4.54 1.50e+00 4.44e-01 9.16e+00 angle pdb=" C2' DC I 131 " pdb=" C1' DC I 131 " pdb=" N1 DC I 131 " ideal model delta sigma weight residual 113.50 117.80 -4.30 1.50e+00 4.44e-01 8.22e+00 ... (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 - 0.028: 1586 0.028 - 0.055: 786 0.055 - 0.083: 311 0.083 - 0.110: 59 0.110 - 0.138: 42 Chirality restraints: 2784 Sorted by residual: chirality pdb=" CA ILE N 94 " pdb=" N ILE N 94 " pdb=" C ILE N 94 " pdb=" CB ILE N 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA VAL M 77 " pdb=" N VAL M 77 " pdb=" C VAL M 77 " pdb=" CB VAL M 77 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE G 111 " pdb=" N ILE G 111 " pdb=" C ILE G 111 " pdb=" CB ILE G 111 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-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: 2.190 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.360 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 : 0.005 0.059 17264 Z= 0.220 Angle : 0.724 7.736 24720 Z= 0.434 Chirality : 0.038 0.138 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 covalent geometry : bond 0.00524 (17260) covalent geometry : angle 0.72432 (24712) SS BOND : bond 0.00378 ( 4) SS BOND : angle 0.85658 ( 8) hydrogen bonds : bond 0.13791 ( 964) hydrogen bonds : angle 4.76345 ( 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 : 0.439 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: 0.8775 time to fit residues: 180.3579 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 : 0.425 ------------------------------------------------------------------------------- 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: 2.9990 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: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN E 113 HIS F 27 GLN F 93 GLN ** M 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.182362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.141476 restraints weight = 16899.647| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.44 r_work: 0.3707 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17264 Z= 0.167 Angle : 0.552 6.343 24720 Z= 0.329 Chirality : 0.036 0.134 2784 Planarity : 0.004 0.035 1996 Dihedral : 28.964 179.540 4910 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.22 % Allowed : 13.20 % Favored : 84.59 % 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: 2.78 (0.22), residues: 548 sheet: 1.49 (0.34), residues: 240 loop : 0.01 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.014 0.001 TYR H 42 PHE 0.009 0.001 PHE A 67 TRP 0.012 0.002 TRP N 196 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00369 (17260) covalent geometry : angle 0.55190 (24712) SS BOND : bond 0.00625 ( 4) SS BOND : angle 1.07947 ( 8) hydrogen bonds : bond 0.04510 ( 964) hydrogen bonds : angle 3.32594 ( 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: 23 poor density : 186 time to evaluate : 0.495 Fit side-chains REVERT: D 35 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.6544 (mm-30) REVERT: E 73 GLU cc_start: 0.8166 (tt0) cc_final: 0.7894 (tt0) REVERT: G 41 GLU cc_start: 0.8461 (tt0) cc_final: 0.8146 (tt0) REVERT: M 80 ARG cc_start: 0.8540 (mtm110) cc_final: 0.8159 (mtm110) REVERT: M 98 GLU cc_start: 0.6266 (mp0) cc_final: 0.5801 (mp0) REVERT: M 152 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7383 (tm-30) REVERT: M 154 GLN cc_start: 0.8257 (tp40) cc_final: 0.7518 (mp10) REVERT: M 165 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7661 (t) REVERT: M 238 GLU cc_start: 0.6982 (pt0) cc_final: 0.6641 (pm20) REVERT: N 23 MET cc_start: 0.9010 (tpt) cc_final: 0.8514 (mmt) REVERT: N 36 GLU cc_start: 0.8000 (pm20) cc_final: 0.7663 (pm20) REVERT: N 80 ARG cc_start: 0.8069 (mtm110) cc_final: 0.7718 (mtp-110) REVERT: N 208 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8252 (ttpt) outliers start: 23 outliers final: 11 residues processed: 195 average time/residue: 0.9650 time to fit residues: 200.9931 Evaluate side-chains 183 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 51 ASP 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 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 165 THR Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 99 SER Chi-restraints excluded: chain N residue 208 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 95 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS B 93 GLN C 24 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN G 89 ASN ** M 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.179242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.138153 restraints weight = 16930.009| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.43 r_work: 0.3670 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17264 Z= 0.198 Angle : 0.560 7.705 24720 Z= 0.333 Chirality : 0.036 0.148 2784 Planarity : 0.004 0.032 1996 Dihedral : 29.006 178.699 4907 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.89 % Allowed : 13.68 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.24), residues: 1198 helix: 2.66 (0.22), residues: 548 sheet: 1.49 (0.34), residues: 240 loop : -0.14 (0.29), residues: 410 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 0.008 0.002 PHE F 61 TRP 0.010 0.002 TRP N 196 HIS 0.004 0.001 HIS N 110 Details of bonding type rmsd covalent geometry : bond 0.00453 (17260) covalent geometry : angle 0.55952 (24712) SS BOND : bond 0.00761 ( 4) SS BOND : angle 1.48718 ( 8) hydrogen bonds : bond 0.05078 ( 964) hydrogen bonds : angle 3.31928 ( 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 209 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.460 Fit side-chains REVERT: B 77 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7793 (mtmt) REVERT: D 35 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.6740 (mm-30) REVERT: E 73 GLU cc_start: 0.8161 (tt0) cc_final: 0.7781 (tt0) REVERT: G 41 GLU cc_start: 0.8431 (tt0) cc_final: 0.8104 (tt0) REVERT: H 42 TYR cc_start: 0.7937 (t80) cc_final: 0.7717 (t80) REVERT: H 76 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: M 80 ARG cc_start: 0.8477 (mtm110) cc_final: 0.8189 (mtm110) REVERT: M 98 GLU cc_start: 0.6302 (mp0) cc_final: 0.5779 (mp0) REVERT: M 154 GLN cc_start: 0.8239 (tp40) cc_final: 0.8007 (tp40) REVERT: M 238 GLU cc_start: 0.6988 (pt0) cc_final: 0.6653 (pm20) REVERT: N 23 MET cc_start: 0.9145 (tpt) cc_final: 0.8933 (mmp) REVERT: N 36 GLU cc_start: 0.7928 (pm20) cc_final: 0.7608 (pm20) REVERT: N 124 GLU cc_start: 0.7316 (pm20) cc_final: 0.7072 (pm20) outliers start: 30 outliers final: 18 residues processed: 189 average time/residue: 0.8494 time to fit residues: 171.9081 Evaluate side-chains 191 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 LYS 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 H residue 51 ASP 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 N residue 99 SER Chi-restraints excluded: chain N residue 152 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 54 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 chunk 118 optimal weight: 0.4980 chunk 126 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN M 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.168881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.122434 restraints weight = 16812.995| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.53 r_work: 0.3416 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17264 Z= 0.187 Angle : 0.543 6.405 24720 Z= 0.325 Chirality : 0.036 0.137 2784 Planarity : 0.004 0.032 1996 Dihedral : 29.039 178.683 4907 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.18 % Allowed : 14.84 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.24), residues: 1198 helix: 2.66 (0.22), residues: 548 sheet: 1.46 (0.34), residues: 240 loop : -0.16 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.013 0.001 TYR H 42 PHE 0.008 0.001 PHE A 67 TRP 0.009 0.001 TRP M 196 HIS 0.004 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00424 (17260) covalent geometry : angle 0.54267 (24712) SS BOND : bond 0.00719 ( 4) SS BOND : angle 1.42829 ( 8) hydrogen bonds : bond 0.04630 ( 964) hydrogen bonds : angle 3.21662 ( 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 204 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.475 Fit side-chains REVERT: B 68 ASP cc_start: 0.8231 (m-30) cc_final: 0.7959 (m-30) REVERT: B 77 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7561 (mtpt) REVERT: C 73 ASN cc_start: 0.7687 (t0) cc_final: 0.7365 (t0) REVERT: D 35 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.6714 (mm-30) REVERT: E 73 GLU cc_start: 0.7935 (tt0) cc_final: 0.7532 (tt0) REVERT: G 41 GLU cc_start: 0.8389 (tt0) cc_final: 0.8035 (tt0) REVERT: H 42 TYR cc_start: 0.7620 (t80) cc_final: 0.7278 (t80) REVERT: H 76 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: M 30 MET cc_start: 0.8128 (ptt) cc_final: 0.7785 (ptt) REVERT: M 80 ARG cc_start: 0.8309 (mtm110) cc_final: 0.7980 (mtm110) REVERT: M 154 GLN cc_start: 0.8115 (tp40) cc_final: 0.7847 (tp40) REVERT: M 200 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8394 (tp) REVERT: M 230 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.6511 (tpt) REVERT: M 238 GLU cc_start: 0.7077 (pt0) cc_final: 0.6832 (pt0) REVERT: N 36 GLU cc_start: 0.7740 (pm20) cc_final: 0.7362 (pm20) REVERT: N 80 ARG cc_start: 0.7955 (mtm110) cc_final: 0.7753 (mtp-110) REVERT: N 208 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8141 (ttpt) outliers start: 33 outliers final: 18 residues processed: 184 average time/residue: 0.9505 time to fit residues: 186.8996 Evaluate side-chains 187 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 40 SER 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 51 ASP 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 M residue 230 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 GLN M 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.167068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120426 restraints weight = 16796.961| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.54 r_work: 0.3405 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17264 Z= 0.220 Angle : 0.572 7.309 24720 Z= 0.340 Chirality : 0.037 0.144 2784 Planarity : 0.004 0.032 1996 Dihedral : 29.130 178.615 4907 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.85 % Allowed : 14.26 % Favored : 81.89 % 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: 2.05 (0.24), residues: 1198 helix: 2.54 (0.22), residues: 546 sheet: 1.37 (0.34), residues: 240 loop : -0.27 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.012 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 M 110 Details of bonding type rmsd covalent geometry : bond 0.00507 (17260) covalent geometry : angle 0.57101 (24712) SS BOND : bond 0.00829 ( 4) SS BOND : angle 1.71774 ( 8) hydrogen bonds : bond 0.05297 ( 964) hydrogen bonds : angle 3.30853 ( 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 208 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 0.468 Fit side-chains REVERT: B 77 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7692 (mtmt) REVERT: C 51 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7497 (tp) REVERT: D 35 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.6755 (mm-30) REVERT: E 73 GLU cc_start: 0.8051 (tt0) cc_final: 0.7654 (tt0) REVERT: G 41 GLU cc_start: 0.8396 (tt0) cc_final: 0.8038 (tt0) REVERT: H 42 TYR cc_start: 0.7706 (t80) cc_final: 0.7391 (t80) REVERT: H 76 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: H 101 LEU cc_start: 0.8641 (mt) cc_final: 0.8318 (mt) REVERT: M 80 ARG cc_start: 0.8359 (mtm110) cc_final: 0.8030 (mtm110) REVERT: M 98 GLU cc_start: 0.6194 (mp0) cc_final: 0.5847 (mp0) REVERT: M 154 GLN cc_start: 0.8095 (tp40) cc_final: 0.7832 (tp40) REVERT: M 200 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8444 (tp) REVERT: M 230 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.6588 (tpt) REVERT: M 238 GLU cc_start: 0.7106 (pt0) cc_final: 0.6897 (pt0) REVERT: M 261 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7780 (pm20) REVERT: N 36 GLU cc_start: 0.7822 (pm20) cc_final: 0.7605 (pm20) REVERT: N 124 GLU cc_start: 0.7320 (pm20) cc_final: 0.7072 (pm20) REVERT: N 208 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8204 (ttpt) outliers start: 40 outliers final: 21 residues processed: 183 average time/residue: 0.9848 time to fit residues: 192.3869 Evaluate side-chains 193 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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 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 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 M residue 230 MET Chi-restraints excluded: chain M residue 261 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 16 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 126 optimal weight: 0.0270 chunk 49 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN M 152 GLN M 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.170423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.124350 restraints weight = 16743.465| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.52 r_work: 0.3449 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17264 Z= 0.143 Angle : 0.524 6.271 24720 Z= 0.317 Chirality : 0.034 0.139 2784 Planarity : 0.004 0.036 1996 Dihedral : 29.080 178.325 4907 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.89 % Allowed : 15.32 % Favored : 81.79 % 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: 2.83 (0.22), residues: 546 sheet: 1.44 (0.34), residues: 240 loop : -0.17 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 71 TYR 0.011 0.001 TYR H 42 PHE 0.008 0.001 PHE A 67 TRP 0.006 0.001 TRP M 185 HIS 0.003 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00309 (17260) covalent geometry : angle 0.52403 (24712) SS BOND : bond 0.00544 ( 4) SS BOND : angle 1.02777 ( 8) hydrogen bonds : bond 0.03966 ( 964) hydrogen bonds : angle 3.17294 ( 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 201 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.373 Fit side-chains REVERT: B 77 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7610 (mtpt) REVERT: D 35 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6722 (mm-30) REVERT: E 73 GLU cc_start: 0.8004 (tt0) cc_final: 0.7593 (tt0) REVERT: G 41 GLU cc_start: 0.8388 (tt0) cc_final: 0.8013 (tt0) REVERT: G 91 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: H 42 TYR cc_start: 0.7599 (t80) cc_final: 0.7216 (t80) REVERT: M 80 ARG cc_start: 0.8323 (mtm110) cc_final: 0.7958 (mtm110) REVERT: M 98 GLU cc_start: 0.6062 (mp0) cc_final: 0.5726 (mp0) REVERT: M 154 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7424 (mp10) REVERT: M 230 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.6499 (tpt) REVERT: N 36 GLU cc_start: 0.7798 (pm20) cc_final: 0.7584 (pm20) REVERT: N 124 GLU cc_start: 0.7272 (pm20) cc_final: 0.7036 (pm20) REVERT: N 195 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: N 208 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8142 (ttpt) outliers start: 30 outliers final: 15 residues processed: 182 average time/residue: 0.9684 time to fit residues: 188.2236 Evaluate side-chains 189 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 M residue 84 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 152 GLN Chi-restraints excluded: chain M residue 154 GLN Chi-restraints excluded: chain M residue 230 MET 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: 4.9990 chunk 11 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 GLN M 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.169144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.122841 restraints weight = 16773.103| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.53 r_work: 0.3433 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17264 Z= 0.176 Angle : 0.537 6.390 24720 Z= 0.322 Chirality : 0.035 0.136 2784 Planarity : 0.004 0.032 1996 Dihedral : 29.026 178.984 4907 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.70 % Allowed : 16.57 % Favored : 80.73 % 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: 2.29 (0.24), residues: 1198 helix: 2.79 (0.22), residues: 546 sheet: 1.42 (0.34), residues: 240 loop : -0.19 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 71 TYR 0.012 0.001 TYR H 42 PHE 0.008 0.001 PHE E 67 TRP 0.007 0.001 TRP M 185 HIS 0.004 0.001 HIS N 110 Details of bonding type rmsd covalent geometry : bond 0.00398 (17260) covalent geometry : angle 0.53613 (24712) SS BOND : bond 0.00652 ( 4) SS BOND : angle 1.32835 ( 8) hydrogen bonds : bond 0.04466 ( 964) hydrogen bonds : angle 3.17346 ( 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 194 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.467 Fit side-chains REVERT: B 77 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7642 (mtpt) REVERT: C 51 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7459 (tp) REVERT: D 35 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.6727 (mm-30) REVERT: E 73 GLU cc_start: 0.8040 (tt0) cc_final: 0.7641 (tt0) REVERT: G 41 GLU cc_start: 0.8388 (tt0) cc_final: 0.8031 (tt0) REVERT: G 91 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7467 (tt0) REVERT: H 42 TYR cc_start: 0.7645 (t80) cc_final: 0.7268 (t80) REVERT: M 80 ARG cc_start: 0.8349 (mtm110) cc_final: 0.7931 (mtm110) REVERT: M 98 GLU cc_start: 0.6081 (mp0) cc_final: 0.5325 (mp0) REVERT: M 152 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7548 (tt0) REVERT: M 154 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7436 (mp10) REVERT: M 200 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8452 (tp) REVERT: M 230 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.6547 (tpt) REVERT: N 36 GLU cc_start: 0.7802 (pm20) cc_final: 0.7580 (pm20) REVERT: N 208 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8177 (ttpt) outliers start: 28 outliers final: 16 residues processed: 177 average time/residue: 0.9836 time to fit residues: 185.7021 Evaluate side-chains 188 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 G residue 91 GLU Chi-restraints excluded: chain M residue 84 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 152 GLN Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 208 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 92 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 119 optimal weight: 0.2980 chunk 147 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.170452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.124215 restraints weight = 16752.752| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.54 r_work: 0.3433 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17264 Z= 0.151 Angle : 0.527 6.366 24720 Z= 0.317 Chirality : 0.034 0.136 2784 Planarity : 0.004 0.035 1996 Dihedral : 29.009 178.881 4907 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.50 % Allowed : 16.67 % Favored : 80.83 % 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: 2.37 (0.24), residues: 1198 helix: 2.86 (0.22), residues: 546 sheet: 1.42 (0.34), residues: 240 loop : -0.14 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 71 TYR 0.010 0.001 TYR H 42 PHE 0.007 0.001 PHE A 67 TRP 0.006 0.001 TRP M 185 HIS 0.003 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00333 (17260) covalent geometry : angle 0.52647 (24712) SS BOND : bond 0.00566 ( 4) SS BOND : angle 1.10964 ( 8) hydrogen bonds : bond 0.04010 ( 964) hydrogen bonds : angle 3.14157 ( 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 193 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.447 Fit side-chains REVERT: B 77 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7567 (mtpt) REVERT: C 51 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7386 (tp) REVERT: D 35 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.6651 (mm-30) REVERT: E 73 GLU cc_start: 0.7944 (tt0) cc_final: 0.7536 (tt0) REVERT: E 115 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7473 (mttp) REVERT: G 41 GLU cc_start: 0.8376 (tt0) cc_final: 0.8008 (tt0) REVERT: G 91 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7358 (tt0) REVERT: H 42 TYR cc_start: 0.7513 (t80) cc_final: 0.7129 (t80) REVERT: M 80 ARG cc_start: 0.8281 (mtm110) cc_final: 0.7843 (mtm110) REVERT: M 98 GLU cc_start: 0.5982 (mp0) cc_final: 0.5228 (mp0) REVERT: M 112 GLU cc_start: 0.6759 (mp0) cc_final: 0.6150 (mt-10) REVERT: M 200 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8410 (tp) REVERT: N 36 GLU cc_start: 0.7769 (pm20) cc_final: 0.7533 (pm20) REVERT: N 124 GLU cc_start: 0.7251 (pm20) cc_final: 0.7035 (pm20) REVERT: N 195 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: N 208 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8140 (ttpt) outliers start: 26 outliers final: 14 residues processed: 177 average time/residue: 0.8582 time to fit residues: 162.3212 Evaluate side-chains 187 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 123 SER Chi-restraints excluded: chain E residue 115 LYS 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 M residue 84 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 63 optimal weight: 0.2980 chunk 76 optimal weight: 4.9990 chunk 56 optimal weight: 0.0470 chunk 143 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4020 r_free = 0.4020 target = 0.170671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124503 restraints weight = 16791.467| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.53 r_work: 0.3449 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17264 Z= 0.143 Angle : 0.525 6.427 24720 Z= 0.316 Chirality : 0.034 0.136 2784 Planarity : 0.004 0.032 1996 Dihedral : 29.002 178.894 4907 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.31 % Allowed : 17.24 % Favored : 80.44 % 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 (0.25), residues: 1198 helix: 2.90 (0.22), residues: 546 sheet: 1.42 (0.34), residues: 240 loop : -0.13 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 71 TYR 0.010 0.001 TYR M 203 PHE 0.007 0.001 PHE A 67 TRP 0.006 0.001 TRP M 185 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00310 (17260) covalent geometry : angle 0.52443 (24712) SS BOND : bond 0.00543 ( 4) SS BOND : angle 1.05709 ( 8) hydrogen bonds : bond 0.03911 ( 964) hydrogen bonds : angle 3.14080 ( 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: 24 poor density : 165 time to evaluate : 0.473 Fit side-chains REVERT: B 77 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7598 (mtpt) REVERT: C 51 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7425 (tp) REVERT: D 35 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6708 (mm-30) REVERT: E 73 GLU cc_start: 0.8022 (tt0) cc_final: 0.7607 (tt0) REVERT: E 115 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7553 (mttp) REVERT: G 41 GLU cc_start: 0.8384 (tt0) cc_final: 0.8021 (tt0) REVERT: G 91 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: H 42 TYR cc_start: 0.7590 (t80) cc_final: 0.7207 (t80) REVERT: M 80 ARG cc_start: 0.8332 (mtm110) cc_final: 0.7901 (mtm110) REVERT: M 98 GLU cc_start: 0.6044 (mp0) cc_final: 0.5296 (mp0) REVERT: M 112 GLU cc_start: 0.6752 (mp0) cc_final: 0.6276 (mt-10) REVERT: M 200 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8452 (tp) REVERT: N 36 GLU cc_start: 0.7796 (pm20) cc_final: 0.7573 (pm20) REVERT: N 124 GLU cc_start: 0.7296 (pm20) cc_final: 0.7058 (pm20) REVERT: N 195 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: N 208 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8174 (ttpt) outliers start: 24 outliers final: 14 residues processed: 175 average time/residue: 0.9409 time to fit residues: 175.7136 Evaluate side-chains 186 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 123 SER Chi-restraints excluded: chain E residue 115 LYS 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 M residue 84 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 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 17 optimal weight: 9.9990 chunk 107 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4012 r_free = 0.4012 target = 0.169958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.123799 restraints weight = 16770.277| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.52 r_work: 0.3444 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17264 Z= 0.164 Angle : 0.529 6.339 24720 Z= 0.318 Chirality : 0.035 0.135 2784 Planarity : 0.004 0.034 1996 Dihedral : 28.969 179.100 4907 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.22 % Allowed : 17.05 % Favored : 80.73 % 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: 2.38 (0.24), residues: 1198 helix: 2.87 (0.22), residues: 546 sheet: 1.43 (0.34), residues: 240 loop : -0.13 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 71 TYR 0.011 0.001 TYR H 42 PHE 0.007 0.001 PHE E 67 TRP 0.007 0.001 TRP M 185 HIS 0.003 0.001 HIS N 110 Details of bonding type rmsd covalent geometry : bond 0.00367 (17260) covalent geometry : angle 0.52904 (24712) SS BOND : bond 0.00618 ( 4) SS BOND : angle 1.26066 ( 8) hydrogen bonds : bond 0.04243 ( 964) hydrogen bonds : angle 3.13537 ( 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 188 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.464 Fit side-chains REVERT: B 77 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7544 (mtpt) REVERT: C 51 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7452 (tp) REVERT: D 35 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.6716 (mm-30) REVERT: E 73 GLU cc_start: 0.8075 (tt0) cc_final: 0.7684 (tt0) REVERT: E 115 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7568 (mttp) REVERT: G 41 GLU cc_start: 0.8379 (tt0) cc_final: 0.8012 (tt0) REVERT: G 91 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: H 42 TYR cc_start: 0.7648 (t80) cc_final: 0.7256 (t80) REVERT: M 80 ARG cc_start: 0.8342 (mtm110) cc_final: 0.7916 (mtm110) REVERT: M 98 GLU cc_start: 0.6070 (mp0) cc_final: 0.5325 (mp0) REVERT: M 112 GLU cc_start: 0.6738 (mp0) cc_final: 0.6273 (mt-10) REVERT: M 200 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8453 (tp) REVERT: N 124 GLU cc_start: 0.7225 (pm20) cc_final: 0.6978 (pm20) REVERT: N 195 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: N 208 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8168 (ttpt) outliers start: 23 outliers final: 14 residues processed: 175 average time/residue: 0.9614 time to fit residues: 179.5354 Evaluate side-chains 186 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 D residue 35 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 115 LYS 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 M residue 84 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 147 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.168073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123853 restraints weight = 15213.212| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.42 r_work: 0.3260 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17264 Z= 0.190 Angle : 0.551 7.055 24720 Z= 0.328 Chirality : 0.036 0.138 2784 Planarity : 0.004 0.034 1996 Dihedral : 29.045 178.586 4907 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.31 % Allowed : 17.15 % Favored : 80.54 % 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: 2.22 (0.24), residues: 1198 helix: 2.74 (0.22), residues: 546 sheet: 1.34 (0.34), residues: 240 loop : -0.20 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 71 TYR 0.012 0.001 TYR H 42 PHE 0.008 0.001 PHE F 61 TRP 0.007 0.001 TRP M 259 HIS 0.004 0.001 HIS N 110 Details of bonding type rmsd covalent geometry : bond 0.00433 (17260) covalent geometry : angle 0.55053 (24712) SS BOND : bond 0.00702 ( 4) SS BOND : angle 1.48398 ( 8) hydrogen bonds : bond 0.04713 ( 964) hydrogen bonds : angle 3.20661 ( 2405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7490.98 seconds wall clock time: 127 minutes 42.52 seconds (7662.52 seconds total)