Starting phenix.real_space_refine on Sat Jul 4 04:29:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubj_42090/07_2026/8ubj_42090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubj_42090/07_2026/8ubj_42090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ubj_42090/07_2026/8ubj_42090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubj_42090/07_2026/8ubj_42090.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ubj_42090/07_2026/8ubj_42090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubj_42090/07_2026/8ubj_42090.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 3.30, per 1000 atoms: 0.20 Number of scatterers: 16288 At special positions: 0 Unit cell: (137.214, 139.755, 144.837, 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: 1.36 Conformation dependent library (CDL) restraints added in 526.5 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, 21.3% beta 162 base pairs and 280 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.972A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) 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: 3.847A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.601A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) 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: 4.291A 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: 3.681A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.867A 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 removed outlier: 3.575A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.903A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 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: 4.323A 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: 3.778A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 4.405A 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: 3.541A 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 removed outlier: 3.524A pdb=" N SER M 240 " --> pdb=" O SER M 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 102 removed outlier: 3.647A 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: 6.887A 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: 7.220A 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 101 through 102 removed outlier: 6.642A 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: 6.912A 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: 7.272A 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 Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 3.791A pdb=" N GLU M 124 " --> pdb=" O MET M 30 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA M 32 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.618A 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: 3.791A pdb=" N GLU M 124 " --> pdb=" O MET M 30 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA M 32 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 3.583A 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: 3.919A pdb=" N GLU M 159 " --> pdb=" O SER M 264 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR M 266 " --> pdb=" O GLU M 159 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL M 161 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.949A 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: 3.919A pdb=" N GLU M 159 " --> pdb=" O SER M 264 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR M 266 " --> pdb=" O GLU M 159 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL M 161 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR M 258 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 25 removed outlier: 3.722A pdb=" N ASP N 89 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 72 through 73 removed outlier: 6.470A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR N 116 " --> pdb=" O GLN N 109 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 72 through 73 removed outlier: 6.470A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (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: 6.584A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.940A 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: 4.043A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 412 hydrogen bonds 824 hydrogen bond angles 0 basepair planarities 162 basepair parallelities 280 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 1.74 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: 3969 1.34 - 1.46: 4945 1.46 - 1.58: 7648 1.58 - 1.70: 646 1.70 - 1.82: 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 1.546 -0.078 1.40e-02 5.10e+03 3.14e+01 bond pdb=" C1' DC J 4 " pdb=" N1 DC J 4 " ideal model delta sigma weight residual 1.468 1.546 -0.078 1.40e-02 5.10e+03 3.14e+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 2.92e+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 1.540 -0.072 1.40e-02 5.10e+03 2.63e+01 ... (remaining 17255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 23634 2.20 - 4.41: 996 4.41 - 6.61: 74 6.61 - 8.82: 5 8.82 - 11.02: 3 Bond angle restraints: 24712 Sorted by residual: angle pdb=" CB LYS H 34 " pdb=" CG LYS H 34 " pdb=" CD LYS H 34 " ideal model delta sigma weight residual 111.30 122.32 -11.02 2.30e+00 1.89e-01 2.30e+01 angle pdb=" O4' DC J 5 " pdb=" C1' DC J 5 " pdb=" N1 DC J 5 " ideal model delta sigma weight residual 108.00 111.10 -3.10 7.00e-01 2.04e+00 1.97e+01 angle pdb=" O4' DT J 143 " pdb=" C4' DT J 143 " pdb=" C3' DT J 143 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 7 " pdb=" C4 DT I 7 " pdb=" O4 DT I 7 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" O5' DC J 4 " pdb=" C5' DC J 4 " pdb=" C4' DC J 4 " ideal model delta sigma weight residual 109.40 112.87 -3.47 8.00e-01 1.56e+00 1.88e+01 ... (remaining 24707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 8126 34.85 - 69.71: 1379 69.71 - 104.56: 39 104.56 - 139.42: 0 139.42 - 174.27: 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 45.73 174.27 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 70.20 149.80 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" C ASP A 81 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " pdb=" CB ASP A 81 " ideal model delta harmonic sigma weight residual -122.60 -131.77 9.17 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 9543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2100 0.052 - 0.104: 341 0.104 - 0.156: 331 0.156 - 0.208: 8 0.208 - 0.259: 4 Chirality restraints: 2784 Sorted by residual: chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB ILE G 62 " pdb=" CA ILE G 62 " pdb=" CG1 ILE G 62 " pdb=" CG2 ILE G 62 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB VAL M 265 " pdb=" CA VAL M 265 " pdb=" CG1 VAL M 265 " pdb=" CG2 VAL M 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2781 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA J 73 " 0.029 2.00e-02 2.50e+03 1.47e-02 5.91e+00 pdb=" N9 DA J 73 " -0.037 2.00e-02 2.50e+03 pdb=" C8 DA J 73 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA J 73 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA J 73 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA J 73 " 0.004 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 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DA J 73 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 23 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C ARG F 23 " 0.039 2.00e-02 2.50e+03 pdb=" O ARG F 23 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP F 24 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 91 " -0.025 2.00e-02 2.50e+03 1.38e-02 4.28e+00 pdb=" N1 DC I 91 " 0.026 2.00e-02 2.50e+03 pdb=" C2 DC I 91 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DC I 91 " 0.012 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 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DC I 91 " 0.011 2.00e-02 2.50e+03 pdb=" C6 DC I 91 " 0.001 2.00e-02 2.50e+03 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1362 2.74 - 3.28: 13761 3.28 - 3.82: 30193 3.82 - 4.36: 36518 4.36 - 4.90: 54822 Nonbonded interactions: 136656 Sorted by model distance: nonbonded pdb=" OD2 ASP M 222 " pdb=" OG SER M 225 " model vdw 2.206 3.040 nonbonded pdb=" O ASN C 73 " pdb=" ND2 ASN C 73 " model vdw 2.207 3.120 nonbonded pdb=" NH1 ARG C 11 " pdb=" O4' DA J 47 " model vdw 2.213 3.120 nonbonded pdb=" N GLU M 124 " pdb=" OE1 GLU M 124 " model vdw 2.263 3.120 nonbonded pdb=" OE1 GLN H 95 " pdb=" NH2 ARG H 99 " model vdw 2.296 3.120 ... (remaining 136651 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.420 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 0.078 17264 Z= 0.585 Angle : 0.890 11.024 24720 Z= 0.707 Chirality : 0.057 0.259 2784 Planarity : 0.005 0.061 1996 Dihedral : 25.563 174.272 7262 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.67 % Allowed : 15.99 % Favored : 83.33 % 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: 2.17 (0.24), residues: 1198 helix: 2.64 (0.22), residues: 538 sheet: 1.17 (0.35), residues: 218 loop : 0.09 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG M 191 TYR 0.021 0.001 TYR H 42 PHE 0.009 0.001 PHE C 25 TRP 0.007 0.001 TRP M 196 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.59 (17260) covalent geometry : angle 0.88999 / 0.71 (24712) SS BOND : bond 0.00383 / 0.19 ( 4) SS BOND : angle 0.55810 / 0.27 ( 8) hydrogen bonds : bond 0.13718 / 9.15 ( 959) hydrogen bonds : angle 4.76535 / 3.47 ( 2414) *********************** 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 234 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 227 time to evaluate : 0.349 Fit side-chains REVERT: E 115 LYS cc_start: 0.8590 (mtmp) cc_final: 0.8309 (mtmm) REVERT: E 123 ASP cc_start: 0.8883 (m-30) cc_final: 0.8491 (m-30) REVERT: F 79 LYS cc_start: 0.8304 (mttt) cc_final: 0.8038 (mtpt) REVERT: H 52 THR cc_start: 0.9046 (m) cc_final: 0.8801 (m) REVERT: H 59 MET cc_start: 0.8635 (tpp) cc_final: 0.8379 (tpp) REVERT: H 85 LYS cc_start: 0.9025 (mmtp) cc_final: 0.8648 (mmtt) REVERT: M 37 ARG cc_start: 0.8308 (mtp85) cc_final: 0.7909 (mtp180) REVERT: M 265 VAL cc_start: 0.8208 (t) cc_final: 0.7899 (p) REVERT: N 152 GLN cc_start: 0.8427 (tt0) cc_final: 0.8080 (tt0) REVERT: N 230 MET cc_start: 0.8526 (tpt) cc_final: 0.8301 (tmm) REVERT: N 239 ASP cc_start: 0.7677 (m-30) cc_final: 0.7345 (m-30) outliers start: 7 outliers final: 1 residues processed: 229 average time/residue: 0.7476 time to fit residues: 184.8367 Evaluate side-chains 202 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN C 38 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN F 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.130914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.089929 restraints weight = 24890.259| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.81 r_work: 0.3138 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17264 Z= 0.217 Angle : 0.670 7.258 24720 Z= 0.394 Chirality : 0.048 0.235 2784 Planarity : 0.005 0.038 1996 Dihedral : 28.711 176.950 4908 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.70 % Allowed : 15.22 % Favored : 82.08 % 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: 2.12 (0.24), residues: 1198 helix: 2.60 (0.22), residues: 546 sheet: 1.42 (0.37), residues: 206 loop : -0.14 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 79 TYR 0.019 0.002 TYR H 42 PHE 0.013 0.002 PHE C 25 TRP 0.012 0.002 TRP M 196 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 (17260) covalent geometry : angle 0.66967 / 0.39 (24712) SS BOND : bond 0.00808 / 0.41 ( 4) SS BOND : angle 1.37253 / 0.66 ( 8) hydrogen bonds : bond 0.05661 / 3.86 ( 959) hydrogen bonds : angle 3.60936 / 2.64 ( 2414) *********************** 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 235 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8148 (t0) cc_final: 0.7779 (t160) REVERT: D 76 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8238 (mm-30) REVERT: D 116 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8182 (tttm) REVERT: E 56 LYS cc_start: 0.8415 (mtpt) cc_final: 0.8165 (ttmm) REVERT: E 123 ASP cc_start: 0.8741 (m-30) cc_final: 0.8275 (m-30) REVERT: F 79 LYS cc_start: 0.8529 (mttt) cc_final: 0.8303 (mtpt) REVERT: F 84 MET cc_start: 0.8439 (mmp) cc_final: 0.8231 (mmt) REVERT: G 15 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7532 (pptt) REVERT: H 34 LYS cc_start: 0.8427 (mmmt) cc_final: 0.8103 (mmmm) REVERT: H 59 MET cc_start: 0.8637 (tpp) cc_final: 0.8331 (tpp) REVERT: H 71 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: H 87 SER cc_start: 0.8274 (m) cc_final: 0.7899 (p) REVERT: M 37 ARG cc_start: 0.8904 (mtp85) cc_final: 0.8565 (mtp180) REVERT: M 160 LEU cc_start: 0.8520 (mm) cc_final: 0.8288 (mm) REVERT: M 238 GLU cc_start: 0.8941 (pt0) cc_final: 0.8479 (pm20) REVERT: N 36 GLU cc_start: 0.7357 (pm20) cc_final: 0.6862 (pm20) REVERT: N 52 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8932 (tp) REVERT: N 98 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7065 (mt-10) REVERT: N 152 GLN cc_start: 0.8502 (tt0) cc_final: 0.8133 (tt0) REVERT: N 195 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8172 (mt-10) REVERT: N 208 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8443 (ttpp) REVERT: N 222 ASP cc_start: 0.7660 (t0) cc_final: 0.7418 (t0) REVERT: N 231 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7619 (mm-30) outliers start: 28 outliers final: 9 residues processed: 220 average time/residue: 0.7325 time to fit residues: 173.8071 Evaluate side-chains 204 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 161 VAL Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 GLU 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: 10.0000 chunk 105 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN N 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.131713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.090518 restraints weight = 25158.708| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.88 r_work: 0.3140 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1527 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= 0.153 Angle : 0.582 5.686 24720 Z= 0.347 Chirality : 0.043 0.229 2784 Planarity : 0.004 0.043 1996 Dihedral : 29.256 176.044 4906 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.50 % Allowed : 16.47 % Favored : 81.02 % 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: 2.83 (0.22), residues: 548 sheet: 1.26 (0.36), residues: 218 loop : -0.09 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 191 TYR 0.014 0.001 TYR H 42 PHE 0.008 0.001 PHE F 61 TRP 0.009 0.001 TRP M 196 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (17260) covalent geometry : angle 0.58209 / 0.35 (24712) SS BOND : bond 0.00508 / 0.26 ( 4) SS BOND : angle 0.89235 / 0.44 ( 8) hydrogen bonds : bond 0.04673 / 3.14 ( 959) hydrogen bonds : angle 3.29860 / 2.41 ( 2414) *********************** 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 232 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8220 (t0) cc_final: 0.7699 (t160) REVERT: D 71 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: D 76 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8111 (mm-30) REVERT: D 116 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8178 (tttm) REVERT: E 56 LYS cc_start: 0.8337 (mtpt) cc_final: 0.8101 (ttmm) REVERT: E 120 MET cc_start: 0.7621 (mmt) cc_final: 0.6992 (mpp) REVERT: E 123 ASP cc_start: 0.8740 (m-30) cc_final: 0.8277 (m-30) REVERT: F 27 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8590 (mp10) REVERT: F 79 LYS cc_start: 0.8475 (mttt) cc_final: 0.8213 (mtpt) REVERT: F 84 MET cc_start: 0.8450 (mmp) cc_final: 0.8206 (mmt) REVERT: G 15 LYS cc_start: 0.7793 (pttp) cc_final: 0.7480 (pptt) REVERT: G 51 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7979 (tp) REVERT: G 73 ASN cc_start: 0.8194 (t0) cc_final: 0.7780 (t0) REVERT: H 34 LYS cc_start: 0.8462 (mmmt) cc_final: 0.8114 (mmmm) REVERT: H 59 MET cc_start: 0.8539 (tpp) cc_final: 0.8296 (tpp) REVERT: M 113 SER cc_start: 0.7182 (OUTLIER) cc_final: 0.6881 (t) REVERT: M 231 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8373 (mm-30) REVERT: M 238 GLU cc_start: 0.8951 (pt0) cc_final: 0.8517 (pm20) REVERT: M 239 ASP cc_start: 0.8338 (m-30) cc_final: 0.8115 (m-30) REVERT: N 152 GLN cc_start: 0.8421 (tt0) cc_final: 0.8031 (tt0) REVERT: N 159 GLU cc_start: 0.8477 (tt0) cc_final: 0.8184 (mt-10) REVERT: N 195 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: N 208 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8267 (mtpp) REVERT: N 222 ASP cc_start: 0.7680 (t0) cc_final: 0.7169 (t0) REVERT: N 231 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7655 (mm-30) outliers start: 26 outliers final: 11 residues processed: 223 average time/residue: 0.7742 time to fit residues: 186.3204 Evaluate side-chains 212 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 GLU 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: 1.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN D 95 GLN G 38 ASN N 95 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.129751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.088291 restraints weight = 24955.257| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.88 r_work: 0.3111 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17264 Z= 0.181 Angle : 0.600 6.020 24720 Z= 0.350 Chirality : 0.044 0.229 2784 Planarity : 0.004 0.040 1996 Dihedral : 29.562 174.313 4906 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.18 % Allowed : 17.05 % Favored : 79.77 % 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: 2.17 (0.24), residues: 1198 helix: 2.79 (0.22), residues: 548 sheet: 1.40 (0.37), residues: 192 loop : -0.25 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 37 TYR 0.017 0.002 TYR H 42 PHE 0.011 0.002 PHE C 25 TRP 0.010 0.001 TRP M 185 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (17260) covalent geometry : angle 0.60008 / 0.35 (24712) SS BOND : bond 0.00682 / 0.35 ( 4) SS BOND : angle 1.26912 / 0.63 ( 8) hydrogen bonds : bond 0.05052 / 3.41 ( 959) hydrogen bonds : angle 3.23701 / 2.37 ( 2414) *********************** 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 238 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7156 (pp20) REVERT: C 73 ASN cc_start: 0.8436 (t0) cc_final: 0.7855 (t160) REVERT: D 71 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: D 76 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8163 (mm-30) REVERT: D 116 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8324 (ttmm) REVERT: E 56 LYS cc_start: 0.8363 (mtpt) cc_final: 0.8131 (ttmm) REVERT: E 123 ASP cc_start: 0.8788 (m-30) cc_final: 0.8350 (m-30) REVERT: E 133 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6741 (mt-10) REVERT: F 79 LYS cc_start: 0.8430 (mttt) cc_final: 0.8153 (mtpt) REVERT: F 84 MET cc_start: 0.8473 (mmp) cc_final: 0.8257 (mmt) REVERT: G 15 LYS cc_start: 0.7874 (pttp) cc_final: 0.7570 (pptt) REVERT: G 51 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8024 (tp) REVERT: G 73 ASN cc_start: 0.8176 (t0) cc_final: 0.7756 (t0) REVERT: H 34 LYS cc_start: 0.8461 (mmmt) cc_final: 0.8108 (mmmm) REVERT: H 86 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7881 (mtt90) REVERT: H 91 SER cc_start: 0.9014 (p) cc_final: 0.8604 (m) REVERT: M 37 ARG cc_start: 0.8896 (mtp85) cc_final: 0.8575 (mtp180) REVERT: M 113 SER cc_start: 0.7288 (OUTLIER) cc_final: 0.7040 (t) REVERT: M 122 LYS cc_start: 0.7788 (tptp) cc_final: 0.7443 (ttmm) REVERT: M 231 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8203 (mm-30) REVERT: M 238 GLU cc_start: 0.8956 (pt0) cc_final: 0.8474 (pm20) REVERT: N 152 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: N 159 GLU cc_start: 0.8427 (tt0) cc_final: 0.8198 (mt-10) REVERT: N 195 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8209 (mt-10) REVERT: N 222 ASP cc_start: 0.7838 (t0) cc_final: 0.7180 (t0) REVERT: N 231 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7620 (mm-30) outliers start: 33 outliers final: 16 residues processed: 222 average time/residue: 0.7955 time to fit residues: 190.4460 Evaluate side-chains 226 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 89 optimal weight: 30.0000 chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 92 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 73 ASN E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN N 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.128211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.087055 restraints weight = 24954.010| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.81 r_work: 0.3094 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17264 Z= 0.237 Angle : 0.644 6.311 24720 Z= 0.366 Chirality : 0.046 0.242 2784 Planarity : 0.004 0.039 1996 Dihedral : 29.784 173.281 4906 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.05 % Allowed : 16.76 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.24), residues: 1198 helix: 2.64 (0.22), residues: 546 sheet: 1.23 (0.37), residues: 192 loop : -0.34 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 191 TYR 0.020 0.002 TYR H 42 PHE 0.013 0.002 PHE C 25 TRP 0.009 0.002 TRP M 185 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.24 (17260) covalent geometry : angle 0.64367 / 0.37 (24712) SS BOND : bond 0.00809 / 0.42 ( 4) SS BOND : angle 1.56935 / 0.77 ( 8) hydrogen bonds : bond 0.05501 / 3.71 ( 959) hydrogen bonds : angle 3.31164 / 2.42 ( 2414) *********************** 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 246 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8332 (tttm) cc_final: 0.8027 (ttmt) REVERT: A 59 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7264 (pp20) REVERT: C 36 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8261 (mptt) REVERT: C 73 ASN cc_start: 0.8525 (t0) cc_final: 0.7926 (t160) REVERT: D 71 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: D 76 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8149 (mm-30) REVERT: D 116 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8347 (ttmm) REVERT: E 56 LYS cc_start: 0.8435 (mtpt) cc_final: 0.8215 (ttmm) REVERT: E 120 MET cc_start: 0.7786 (mmt) cc_final: 0.7490 (mpp) REVERT: E 133 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6937 (mt-10) REVERT: F 53 GLU cc_start: 0.8556 (tp30) cc_final: 0.8233 (mp0) REVERT: F 79 LYS cc_start: 0.8436 (mttt) cc_final: 0.8152 (mtpt) REVERT: G 15 LYS cc_start: 0.7915 (pttp) cc_final: 0.7601 (pptt) REVERT: G 51 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7994 (tp) REVERT: G 73 ASN cc_start: 0.8261 (t0) cc_final: 0.7923 (t0) REVERT: G 99 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8001 (mtt90) REVERT: H 34 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8198 (mmmm) REVERT: H 86 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7966 (mtt90) REVERT: M 37 ARG cc_start: 0.8961 (mtp85) cc_final: 0.8705 (mtp180) REVERT: M 89 ASP cc_start: 0.8185 (t0) cc_final: 0.7862 (p0) REVERT: M 122 LYS cc_start: 0.7823 (tptp) cc_final: 0.7408 (mtpp) REVERT: M 231 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8110 (mm-30) REVERT: M 238 GLU cc_start: 0.8974 (pt0) cc_final: 0.8505 (pm20) REVERT: N 36 GLU cc_start: 0.7194 (pm20) cc_final: 0.6651 (pm20) REVERT: N 150 GLU cc_start: 0.6404 (pm20) cc_final: 0.6167 (pm20) REVERT: N 152 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: N 159 GLU cc_start: 0.8443 (tt0) cc_final: 0.8236 (mt-10) REVERT: N 195 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8217 (mt-10) REVERT: N 222 ASP cc_start: 0.7916 (t0) cc_final: 0.7149 (t0) REVERT: N 231 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7566 (mm-30) outliers start: 42 outliers final: 21 residues processed: 223 average time/residue: 0.7716 time to fit residues: 185.5306 Evaluate side-chains 230 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 16 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN N 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.129616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.088343 restraints weight = 24779.026| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.87 r_work: 0.3109 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17264 Z= 0.150 Angle : 0.595 5.898 24720 Z= 0.344 Chirality : 0.043 0.233 2784 Planarity : 0.004 0.054 1996 Dihedral : 29.773 173.248 4906 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.60 % Allowed : 18.50 % Favored : 78.90 % 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: 2.11 (0.24), residues: 1198 helix: 2.82 (0.22), residues: 546 sheet: 1.30 (0.37), residues: 192 loop : -0.33 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 191 TYR 0.015 0.001 TYR H 42 PHE 0.007 0.001 PHE F 61 TRP 0.007 0.001 TRP M 196 HIS 0.005 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (17260) covalent geometry : angle 0.59488 / 0.34 (24712) SS BOND : bond 0.00586 / 0.30 ( 4) SS BOND : angle 1.08270 / 0.56 ( 8) hydrogen bonds : bond 0.04543 / 3.06 ( 959) hydrogen bonds : angle 3.16309 / 2.31 ( 2414) *********************** 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 234 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8275 (tttm) cc_final: 0.7984 (ttmp) REVERT: A 59 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7128 (pp20) REVERT: A 76 GLN cc_start: 0.8461 (tt0) cc_final: 0.8181 (tt0) REVERT: C 73 ASN cc_start: 0.8465 (t0) cc_final: 0.7849 (t160) REVERT: D 76 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8090 (mm-30) REVERT: D 116 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8311 (ttmm) REVERT: E 56 LYS cc_start: 0.8335 (mtpt) cc_final: 0.8118 (ttmm) REVERT: E 115 LYS cc_start: 0.9018 (mtmp) cc_final: 0.8647 (mptp) REVERT: E 133 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6718 (mt-10) REVERT: F 27 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8700 (mp10) REVERT: F 79 LYS cc_start: 0.8416 (mttt) cc_final: 0.8105 (mtpt) REVERT: G 15 LYS cc_start: 0.7841 (pttp) cc_final: 0.7572 (pptt) REVERT: G 51 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7930 (tp) REVERT: G 73 ASN cc_start: 0.8242 (t0) cc_final: 0.7989 (t0) REVERT: H 34 LYS cc_start: 0.8464 (mmmt) cc_final: 0.8184 (mmmm) REVERT: H 86 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7853 (mtt90) REVERT: M 89 ASP cc_start: 0.8213 (t0) cc_final: 0.7824 (p0) REVERT: M 122 LYS cc_start: 0.7766 (tptp) cc_final: 0.7388 (mtpp) REVERT: M 230 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8083 (ttm) REVERT: M 231 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8063 (mm-30) REVERT: M 238 GLU cc_start: 0.8966 (pt0) cc_final: 0.8481 (pm20) REVERT: M 239 ASP cc_start: 0.8480 (m-30) cc_final: 0.8244 (m-30) REVERT: N 36 GLU cc_start: 0.7084 (pm20) cc_final: 0.6557 (pm20) REVERT: N 113 SER cc_start: 0.8604 (t) cc_final: 0.8222 (p) REVERT: N 150 GLU cc_start: 0.6359 (pm20) cc_final: 0.6069 (pm20) REVERT: N 152 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8046 (tt0) REVERT: N 159 GLU cc_start: 0.8398 (tt0) cc_final: 0.8196 (mt-10) REVERT: N 195 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8200 (mt-10) REVERT: N 222 ASP cc_start: 0.7867 (t0) cc_final: 0.7055 (t0) REVERT: N 231 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7571 (mm-30) outliers start: 27 outliers final: 15 residues processed: 220 average time/residue: 0.7474 time to fit residues: 177.1716 Evaluate side-chains 218 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 129 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN N 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.128397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.087133 restraints weight = 24907.701| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.86 r_work: 0.3083 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17264 Z= 0.204 Angle : 0.626 8.118 24720 Z= 0.357 Chirality : 0.045 0.237 2784 Planarity : 0.004 0.054 1996 Dihedral : 29.832 173.332 4906 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.56 % Allowed : 18.30 % Favored : 78.13 % 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: 2.03 (0.24), residues: 1198 helix: 2.69 (0.22), residues: 546 sheet: 1.31 (0.37), residues: 192 loop : -0.32 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 191 TYR 0.020 0.002 TYR H 42 PHE 0.012 0.002 PHE C 25 TRP 0.010 0.002 TRP M 185 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (17260) covalent geometry : angle 0.62537 / 0.36 (24712) SS BOND : bond 0.00735 / 0.38 ( 4) SS BOND : angle 1.46950 / 0.73 ( 8) hydrogen bonds : bond 0.05207 / 3.52 ( 959) hydrogen bonds : angle 3.22153 / 2.35 ( 2414) *********************** 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 236 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.506 Fit side-chains REVERT: A 56 LYS cc_start: 0.8327 (tttm) cc_final: 0.8019 (ttmt) REVERT: A 59 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7221 (pp20) REVERT: A 76 GLN cc_start: 0.8594 (tt0) cc_final: 0.8314 (tt0) REVERT: C 73 ASN cc_start: 0.8539 (t0) cc_final: 0.7812 (t0) REVERT: D 76 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8150 (mm-30) REVERT: D 116 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8343 (ttmm) REVERT: E 56 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8198 (ttmm) REVERT: E 115 LYS cc_start: 0.9052 (mtmp) cc_final: 0.8721 (mptp) REVERT: E 133 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6735 (mt-10) REVERT: F 27 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8734 (mp10) REVERT: F 53 GLU cc_start: 0.8537 (tp30) cc_final: 0.8239 (mp0) REVERT: F 79 LYS cc_start: 0.8433 (mttt) cc_final: 0.8147 (mtpt) REVERT: G 15 LYS cc_start: 0.7901 (pttp) cc_final: 0.7620 (pptt) REVERT: G 51 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8034 (tp) REVERT: H 34 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8193 (mmmm) REVERT: H 86 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7913 (mtt90) REVERT: M 19 MET cc_start: 0.6195 (pmm) cc_final: 0.5587 (pmm) REVERT: M 20 ASP cc_start: 0.8718 (m-30) cc_final: 0.8105 (m-30) REVERT: M 28 SER cc_start: 0.8632 (m) cc_final: 0.8205 (p) REVERT: M 46 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7182 (mt0) REVERT: M 89 ASP cc_start: 0.8231 (t0) cc_final: 0.7918 (p0) REVERT: M 122 LYS cc_start: 0.7769 (tptp) cc_final: 0.7409 (mtpp) REVERT: M 231 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8016 (mm-30) REVERT: M 238 GLU cc_start: 0.8954 (pt0) cc_final: 0.8524 (pm20) REVERT: N 113 SER cc_start: 0.8611 (t) cc_final: 0.8228 (p) REVERT: N 152 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: N 195 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8222 (mt-10) REVERT: N 222 ASP cc_start: 0.7975 (t0) cc_final: 0.7233 (t0) outliers start: 37 outliers final: 22 residues processed: 214 average time/residue: 0.7336 time to fit residues: 169.5335 Evaluate side-chains 227 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 46 GLN Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 GLU 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: 0.8980 chunk 119 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 88 optimal weight: 30.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 38 ASN N 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.128858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.087420 restraints weight = 24825.873| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.87 r_work: 0.3093 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2291 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= 0.161 Angle : 0.615 11.871 24720 Z= 0.351 Chirality : 0.044 0.232 2784 Planarity : 0.004 0.064 1996 Dihedral : 29.832 173.371 4906 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.56 % Allowed : 18.88 % Favored : 77.55 % 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: 2.10 (0.24), residues: 1198 helix: 2.78 (0.22), residues: 544 sheet: 1.33 (0.37), residues: 192 loop : -0.31 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 191 TYR 0.016 0.001 TYR H 42 PHE 0.009 0.001 PHE C 25 TRP 0.009 0.001 TRP M 185 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (17260) covalent geometry : angle 0.61440 / 0.35 (24712) SS BOND : bond 0.00687 / 0.35 ( 4) SS BOND : angle 1.25434 / 0.63 ( 8) hydrogen bonds : bond 0.04841 / 3.27 ( 959) hydrogen bonds : angle 3.19386 / 2.33 ( 2414) *********************** 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 232 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.290 Fit side-chains REVERT: A 56 LYS cc_start: 0.8212 (tttm) cc_final: 0.7914 (ttmp) REVERT: A 59 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7080 (pp20) REVERT: A 76 GLN cc_start: 0.8459 (tt0) cc_final: 0.8179 (tt0) REVERT: C 73 ASN cc_start: 0.8458 (t0) cc_final: 0.7736 (t0) REVERT: C 91 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7668 (tp30) REVERT: D 76 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8064 (mm-30) REVERT: D 116 LYS cc_start: 0.8594 (ttmm) cc_final: 0.8237 (ttmm) REVERT: E 56 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8100 (ttmm) REVERT: E 115 LYS cc_start: 0.8982 (mtmp) cc_final: 0.8652 (mptp) REVERT: E 120 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.6947 (mtp) REVERT: E 133 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6566 (mt-10) REVERT: F 27 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8685 (mp10) REVERT: F 79 LYS cc_start: 0.8346 (mttt) cc_final: 0.8062 (mtpt) REVERT: G 15 LYS cc_start: 0.7824 (pttp) cc_final: 0.7501 (pptt) REVERT: G 51 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7885 (tp) REVERT: G 99 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7934 (mtt90) REVERT: H 34 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8172 (mmmm) REVERT: H 86 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7790 (mtt90) REVERT: M 19 MET cc_start: 0.6244 (pmm) cc_final: 0.5552 (pmm) REVERT: M 20 ASP cc_start: 0.8729 (m-30) cc_final: 0.8022 (m-30) REVERT: M 28 SER cc_start: 0.8583 (m) cc_final: 0.8155 (p) REVERT: M 46 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7073 (mt0) REVERT: M 52 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8702 (tp) REVERT: M 89 ASP cc_start: 0.8170 (t0) cc_final: 0.7834 (p0) REVERT: M 122 LYS cc_start: 0.7670 (tptp) cc_final: 0.7311 (mtpp) REVERT: M 230 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8074 (ttm) REVERT: M 231 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7955 (mm-30) REVERT: M 238 GLU cc_start: 0.8981 (pt0) cc_final: 0.8498 (pm20) REVERT: M 239 ASP cc_start: 0.8423 (m-30) cc_final: 0.8173 (m-30) REVERT: N 152 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: N 195 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: N 222 ASP cc_start: 0.7850 (t0) cc_final: 0.7087 (t0) outliers start: 37 outliers final: 20 residues processed: 214 average time/residue: 0.7026 time to fit residues: 162.6832 Evaluate side-chains 228 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 46 GLN Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 0.0770 chunk 63 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.129502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.088129 restraints weight = 24879.784| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.88 r_work: 0.3106 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17264 Z= 0.138 Angle : 0.609 8.870 24720 Z= 0.349 Chirality : 0.044 0.229 2784 Planarity : 0.004 0.079 1996 Dihedral : 29.819 173.589 4906 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.18 % Allowed : 19.56 % Favored : 77.26 % 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: 2.17 (0.24), residues: 1198 helix: 2.84 (0.22), residues: 546 sheet: 1.36 (0.37), residues: 192 loop : -0.29 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 191 TYR 0.023 0.001 TYR H 42 PHE 0.008 0.001 PHE A 67 TRP 0.008 0.001 TRP M 185 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (17260) covalent geometry : angle 0.60891 / 0.35 (24712) SS BOND : bond 0.00588 / 0.30 ( 4) SS BOND : angle 0.99365 / 0.51 ( 8) hydrogen bonds : bond 0.04521 / 3.04 ( 959) hydrogen bonds : angle 3.15267 / 2.31 ( 2414) *********************** 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 230 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.392 Fit side-chains REVERT: A 56 LYS cc_start: 0.8284 (tttm) cc_final: 0.7992 (ttmp) REVERT: A 59 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7137 (pp20) REVERT: A 76 GLN cc_start: 0.8472 (tt0) cc_final: 0.8187 (tt0) REVERT: C 73 ASN cc_start: 0.8515 (t0) cc_final: 0.7782 (t0) REVERT: C 91 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7742 (tp30) REVERT: D 76 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8102 (mm-30) REVERT: D 116 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8311 (ttmm) REVERT: E 56 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8152 (ttmm) REVERT: E 115 LYS cc_start: 0.9028 (mtmp) cc_final: 0.8713 (mptp) REVERT: E 120 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7142 (mtp) REVERT: F 79 LYS cc_start: 0.8428 (mttt) cc_final: 0.8146 (mtpt) REVERT: G 15 LYS cc_start: 0.7851 (pttp) cc_final: 0.7565 (pptt) REVERT: G 51 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7925 (tp) REVERT: G 99 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7966 (mtt90) REVERT: H 34 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8171 (mmmm) REVERT: H 86 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7794 (mtt90) REVERT: M 19 MET cc_start: 0.6265 (pmm) cc_final: 0.5606 (pmm) REVERT: M 20 ASP cc_start: 0.8719 (m-30) cc_final: 0.8040 (m-30) REVERT: M 28 SER cc_start: 0.8553 (m) cc_final: 0.8147 (p) REVERT: M 46 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7116 (mt0) REVERT: M 89 ASP cc_start: 0.8192 (t0) cc_final: 0.7879 (p0) REVERT: M 122 LYS cc_start: 0.7737 (tptp) cc_final: 0.7380 (mtpp) REVERT: M 230 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8003 (ttm) REVERT: M 231 GLU cc_start: 0.8604 (mm-30) cc_final: 0.7996 (mm-30) REVERT: M 238 GLU cc_start: 0.8952 (pt0) cc_final: 0.8503 (pm20) REVERT: M 239 ASP cc_start: 0.8461 (m-30) cc_final: 0.8222 (m-30) REVERT: N 152 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: N 195 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8200 (mt-10) REVERT: N 222 ASP cc_start: 0.7911 (t0) cc_final: 0.7142 (t0) outliers start: 33 outliers final: 17 residues processed: 212 average time/residue: 0.7394 time to fit residues: 169.1705 Evaluate side-chains 224 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 46 GLN Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 17 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN N 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.129669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.088358 restraints weight = 24865.006| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.87 r_work: 0.3108 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17264 Z= 0.147 Angle : 0.600 10.439 24720 Z= 0.345 Chirality : 0.043 0.228 2784 Planarity : 0.004 0.072 1996 Dihedral : 29.809 173.674 4906 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.50 % Allowed : 20.33 % Favored : 77.17 % 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: 2.18 (0.24), residues: 1198 helix: 2.85 (0.22), residues: 546 sheet: 1.37 (0.37), residues: 192 loop : -0.29 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG M 191 TYR 0.013 0.001 TYR H 42 PHE 0.007 0.001 PHE A 67 TRP 0.007 0.001 TRP M 196 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 (17260) covalent geometry : angle 0.60011 / 0.34 (24712) SS BOND : bond 0.00583 / 0.30 ( 4) SS BOND : angle 1.04489 / 0.53 ( 8) hydrogen bonds : bond 0.04439 / 2.99 ( 959) hydrogen bonds : angle 3.11833 / 2.28 ( 2414) ********************** 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 218 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.489 Fit side-chains REVERT: A 56 LYS cc_start: 0.8285 (tttm) cc_final: 0.7994 (ttmp) REVERT: A 59 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7064 (pp20) REVERT: A 76 GLN cc_start: 0.8475 (tt0) cc_final: 0.8192 (tt0) REVERT: C 73 ASN cc_start: 0.8510 (t0) cc_final: 0.7785 (t0) REVERT: C 91 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7741 (tp30) REVERT: D 76 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8100 (mm-30) REVERT: D 116 LYS cc_start: 0.8673 (ttmm) cc_final: 0.8302 (ttmm) REVERT: E 56 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8157 (ttmm) REVERT: E 115 LYS cc_start: 0.9023 (mtmp) cc_final: 0.8717 (mptp) REVERT: E 120 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7264 (mtp) REVERT: F 79 LYS cc_start: 0.8441 (mttt) cc_final: 0.8157 (mtpt) REVERT: G 15 LYS cc_start: 0.7849 (pttp) cc_final: 0.7568 (pptt) REVERT: G 51 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7936 (tp) REVERT: G 99 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7968 (mtt90) REVERT: H 34 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8163 (mmmm) REVERT: H 86 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7805 (mtt90) REVERT: M 19 MET cc_start: 0.6181 (pmm) cc_final: 0.5564 (pmm) REVERT: M 20 ASP cc_start: 0.8729 (m-30) cc_final: 0.8045 (m-30) REVERT: M 28 SER cc_start: 0.8384 (m) cc_final: 0.7964 (p) REVERT: M 89 ASP cc_start: 0.8197 (t0) cc_final: 0.7883 (p0) REVERT: M 122 LYS cc_start: 0.7773 (tptp) cc_final: 0.7419 (mtpp) REVERT: M 230 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8011 (ttm) REVERT: M 231 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8019 (mm-30) REVERT: M 238 GLU cc_start: 0.8950 (pt0) cc_final: 0.8510 (pm20) REVERT: N 152 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: N 195 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: N 222 ASP cc_start: 0.7922 (t0) cc_final: 0.7150 (t0) outliers start: 26 outliers final: 16 residues processed: 203 average time/residue: 0.7678 time to fit residues: 167.9362 Evaluate side-chains 217 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 195 GLU 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: 10.0000 chunk 117 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.129953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.088706 restraints weight = 24765.924| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.87 r_work: 0.3113 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17264 Z= 0.138 Angle : 0.591 9.459 24720 Z= 0.341 Chirality : 0.043 0.227 2784 Planarity : 0.004 0.070 1996 Dihedral : 29.787 173.939 4906 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.31 % Allowed : 20.71 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.24), residues: 1198 helix: 2.87 (0.22), residues: 546 sheet: 1.40 (0.37), residues: 192 loop : -0.27 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG M 191 TYR 0.018 0.001 TYR H 42 PHE 0.008 0.001 PHE A 67 TRP 0.007 0.001 TRP M 196 HIS 0.004 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (17260) covalent geometry : angle 0.59130 / 0.34 (24712) SS BOND : bond 0.00540 / 0.28 ( 4) SS BOND : angle 0.99189 / 0.51 ( 8) hydrogen bonds : bond 0.04341 / 2.92 ( 959) hydrogen bonds : angle 3.09601 / 2.27 ( 2414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6540.52 seconds wall clock time: 111 minutes 35.74 seconds (6695.74 seconds total)