Starting phenix.real_space_refine on Fri Jul 3 10:15:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8of4_16845/07_2026/8of4_16845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8of4_16845/07_2026/8of4_16845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8of4_16845/07_2026/8of4_16845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8of4_16845/07_2026/8of4_16845.map" model { file = "/net/cci-nas-00/data/ceres_data/8of4_16845/07_2026/8of4_16845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8of4_16845/07_2026/8of4_16845.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8of4_16845/07_2026/8of4_16845.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8of4_16845/07_2026/8of4_16845.cif" } resolution = 2.94 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= 0.010 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 288 5.49 5 S 21 5.16 5 C 7933 2.51 5 N 2664 2.21 5 O 3180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 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: 14087 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} 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: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 916 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "D" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 785 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 785 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "L" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1850 Classifications: {'peptide': 237} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12968 SG CYS L 141 43.940 64.998 46.759 1.00 66.29 S ATOM 12988 SG CYS L 144 43.083 62.071 45.610 1.00 61.78 S ATOM 13153 SG CYS L 166 41.246 63.788 49.455 1.00 72.90 S ATOM 13231 SG CYS L 177 44.562 61.755 48.746 1.00 71.13 S Time building chain proxies: 2.38, per 1000 atoms: 0.17 Number of scatterers: 14087 At special positions: 0 Unit cell: (110.836, 118.164, 121.828, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 21 16.00 P 288 15.00 O 3180 8.00 N 2664 7.00 C 7933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 488.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 144 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 177 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 141 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 166 " Number of angles added : 6 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 63.1% alpha, 4.2% beta 141 base pairs and 258 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.521A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.786A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 5 through 11 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: 4.293A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.663A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.595A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.588A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N THR D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.985A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.578A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.509A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.535A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.311A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.637A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.738A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 44 Processing helix chain 'L' and resid 52 through 58 removed outlier: 4.444A pdb=" N SER L 56 " --> pdb=" O GLY L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 104 Processing helix chain 'L' and resid 117 through 122 Processing helix chain 'L' and resid 125 through 127 No H-bonds generated for 'chain 'L' and resid 125 through 127' Processing helix chain 'L' and resid 193 through 206 Processing helix chain 'L' and resid 221 through 223 No H-bonds generated for 'chain 'L' and resid 221 through 223' Processing helix chain 'L' and resid 224 through 232 removed outlier: 3.745A pdb=" N ALA L 228 " --> pdb=" O ASN L 224 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR L 229 " --> pdb=" O LEU L 225 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS L 230 " --> pdb=" O PRO L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 250 removed outlier: 4.150A pdb=" N ALA L 250 " --> pdb=" O ASP L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 269 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.840A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.733A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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: 6.737A 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: 6.898A 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: 7.060A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 'L' and resid 129 through 131 removed outlier: 6.728A pdb=" N VAL L 47 " --> pdb=" O PHE L 109 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL L 111 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N PHE L 49 " --> pdb=" O VAL L 111 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL L 48 " --> pdb=" O ILE L 211 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU L 213 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS L 50 " --> pdb=" O LEU L 213 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER L 210 " --> pdb=" O VAL L 237 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL L 239 " --> pdb=" O SER L 210 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR L 212 " --> pdb=" O VAL L 239 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU L 236 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE L 254 " --> pdb=" O LEU L 236 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE L 238 " --> pdb=" O ILE L 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 139 through 141 455 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 258 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3203 1.33 - 1.46: 4238 1.46 - 1.58: 6863 1.58 - 1.70: 580 1.70 - 1.82: 37 Bond restraints: 14921 Sorted by residual: bond pdb=" C5 DT I -65 " pdb=" C7 DT I -65 " ideal model delta sigma weight residual 1.500 1.817 -0.317 2.00e-02 2.50e+03 2.52e+02 bond pdb=" C5 DT I -59 " pdb=" C7 DT I -59 " ideal model delta sigma weight residual 1.500 1.662 -0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" C5' DA I -67 " pdb=" C4' DA I -67 " ideal model delta sigma weight residual 1.512 1.552 -0.040 7.00e-03 2.04e+04 3.23e+01 bond pdb=" C5' DT J 66 " pdb=" C4' DT J 66 " ideal model delta sigma weight residual 1.512 1.548 -0.036 7.00e-03 2.04e+04 2.59e+01 bond pdb=" N LYS C 119 " pdb=" CA LYS C 119 " ideal model delta sigma weight residual 1.454 1.517 -0.063 1.27e-02 6.20e+03 2.45e+01 ... (remaining 14916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.50: 21376 12.50 - 25.01: 1 25.01 - 37.51: 1 37.51 - 50.01: 0 50.01 - 62.52: 1 Bond angle restraints: 21379 Sorted by residual: angle pdb=" O LYS C 118 " pdb=" C LYS C 118 " pdb=" N LYS C 119 " ideal model delta sigma weight residual 122.96 60.44 62.52 1.26e+00 6.30e-01 2.46e+03 angle pdb=" O SER C 122 " pdb=" C SER C 122 " pdb=" N ALA C 123 " ideal model delta sigma weight residual 122.04 95.03 27.01 1.35e+00 5.49e-01 4.00e+02 angle pdb=" O5' DC I -32 " pdb=" C5' DC I -32 " pdb=" C4' DC I -32 " ideal model delta sigma weight residual 109.40 120.07 -10.67 8.00e-01 1.56e+00 1.78e+02 angle pdb=" O5' DC I 51 " pdb=" C5' DC I 51 " pdb=" C4' DC I 51 " ideal model delta sigma weight residual 109.40 119.78 -10.38 8.00e-01 1.56e+00 1.68e+02 angle pdb=" O5' DG J 23 " pdb=" C5' DG J 23 " pdb=" C4' DG J 23 " ideal model delta sigma weight residual 109.40 119.57 -10.17 8.00e-01 1.56e+00 1.62e+02 ... (remaining 21374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 6991 33.84 - 67.68: 1230 67.68 - 101.51: 49 101.51 - 135.35: 1 135.35 - 169.19: 3 Dihedral angle restraints: 8274 sinusoidal: 5309 harmonic: 2965 Sorted by residual: dihedral pdb=" CA LYS C 118 " pdb=" C LYS C 118 " pdb=" N LYS C 119 " pdb=" CA LYS C 119 " ideal model delta harmonic sigma weight residual -180.00 -151.20 -28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA THR L 215 " pdb=" C THR L 215 " pdb=" N SER L 216 " pdb=" CA SER L 216 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA LEU L 186 " pdb=" C LEU L 186 " pdb=" N ASP L 187 " pdb=" CA ASP L 187 " ideal model delta harmonic sigma weight residual -180.00 -151.26 -28.74 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 8271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 1966 0.115 - 0.230: 401 0.230 - 0.345: 46 0.345 - 0.460: 14 0.460 - 0.575: 2 Chirality restraints: 2429 Sorted by residual: chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.16 -0.58 2.00e-01 2.50e+01 8.28e+00 chirality pdb=" C3' DG J 20 " pdb=" C4' DG J 20 " pdb=" O3' DG J 20 " pdb=" C2' DG J 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.22 -0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" C3' DA J 65 " pdb=" C4' DA J 65 " pdb=" O3' DA J 65 " pdb=" C2' DA J 65 " both_signs ideal model delta sigma weight residual False -2.73 -2.29 -0.44 2.00e-01 2.50e+01 4.81e+00 ... (remaining 2426 not shown) Planarity restraints: 1708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 70 " -0.449 2.00e-02 2.50e+03 1.88e-01 1.05e+03 pdb=" N9 DG J 70 " 0.082 2.00e-02 2.50e+03 pdb=" C8 DG J 70 " 0.228 2.00e-02 2.50e+03 pdb=" N7 DG J 70 " 0.178 2.00e-02 2.50e+03 pdb=" C5 DG J 70 " 0.064 2.00e-02 2.50e+03 pdb=" C6 DG J 70 " -0.085 2.00e-02 2.50e+03 pdb=" O6 DG J 70 " -0.276 2.00e-02 2.50e+03 pdb=" N1 DG J 70 " -0.052 2.00e-02 2.50e+03 pdb=" C2 DG J 70 " 0.013 2.00e-02 2.50e+03 pdb=" N2 DG J 70 " 0.178 2.00e-02 2.50e+03 pdb=" N3 DG J 70 " 0.039 2.00e-02 2.50e+03 pdb=" C4 DG J 70 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 118 " 0.193 2.00e-02 2.50e+03 2.79e-01 7.76e+02 pdb=" C LYS C 118 " -0.481 2.00e-02 2.50e+03 pdb=" O LYS C 118 " 0.136 2.00e-02 2.50e+03 pdb=" N LYS C 119 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -6 " 0.314 2.00e-02 2.50e+03 1.54e-01 5.93e+02 pdb=" N1 DT I -6 " -0.033 2.00e-02 2.50e+03 pdb=" C2 DT I -6 " -0.089 2.00e-02 2.50e+03 pdb=" O2 DT I -6 " -0.187 2.00e-02 2.50e+03 pdb=" N3 DT I -6 " -0.025 2.00e-02 2.50e+03 pdb=" C4 DT I -6 " 0.059 2.00e-02 2.50e+03 pdb=" O4 DT I -6 " 0.246 2.00e-02 2.50e+03 pdb=" C5 DT I -6 " -0.063 2.00e-02 2.50e+03 pdb=" C7 DT I -6 " -0.133 2.00e-02 2.50e+03 pdb=" C6 DT I -6 " -0.089 2.00e-02 2.50e+03 ... (remaining 1705 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 5401 2.97 - 3.45: 14075 3.45 - 3.93: 26652 3.93 - 4.42: 29933 4.42 - 4.90: 41949 Nonbonded interactions: 118010 Sorted by model distance: nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 75 " model vdw 2.486 3.040 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 75 " model vdw 2.490 3.040 nonbonded pdb=" O LYS C 118 " pdb=" CA LYS C 119 " model vdw 2.511 2.776 nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 2.550 3.040 nonbonded pdb=" OG SER B 47 " pdb=" OP1 DC J 7 " model vdw 2.572 3.040 ... (remaining 118005 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' and resid 20 through 102) } ncs_group { reference = (chain 'C' and resid 12 through 119) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.340 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 0.015 0.558 14925 Z= 1.297 Angle : 2.001 62.518 21385 Z= 1.963 Chirality : 0.097 0.575 2429 Planarity : 0.031 0.279 1708 Dihedral : 25.752 169.188 6360 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.58 % Allowed : 2.80 % Favored : 96.62 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.24), residues: 1009 helix: 0.25 (0.19), residues: 610 sheet: -1.00 (0.95), residues: 35 loop : -0.79 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG D 27 TYR 0.143 0.017 TYR C 57 PHE 0.048 0.013 PHE D 67 TRP 0.250 0.042 TRP L 276 HIS 0.013 0.003 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.01380 / 1.28 (14921) covalent geometry : angle 1.98770 / 1.96 (21379) hydrogen bonds : bond 0.14471 / 9.99 ( 809) hydrogen bonds : angle 6.19379 / 4.44 ( 2043) metal coordination : bond 0.32596 / 17.23 ( 4) metal coordination : angle 14.00908 / 7.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 269 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7937 (tt0) cc_final: 0.7675 (tt0) REVERT: A 90 MET cc_start: 0.7478 (mmp) cc_final: 0.7257 (mmp) REVERT: A 105 GLU cc_start: 0.7502 (tt0) cc_final: 0.7300 (mt-10) REVERT: B 84 MET cc_start: 0.8093 (mmp) cc_final: 0.7850 (mmp) REVERT: D 59 MET cc_start: 0.8475 (mmm) cc_final: 0.8210 (mmp) REVERT: F 35 ARG cc_start: 0.7647 (mtp85) cc_final: 0.7307 (mtp85) REVERT: H 75 SER cc_start: 0.8778 (t) cc_final: 0.8545 (t) REVERT: H 96 ARG cc_start: 0.8472 (tpp80) cc_final: 0.7954 (ttt-90) REVERT: H 112 THR cc_start: 0.8798 (t) cc_final: 0.8454 (p) REVERT: L 49 PHE cc_start: 0.6716 (m-80) cc_final: 0.6323 (m-80) REVERT: L 55 ILE cc_start: 0.3933 (OUTLIER) cc_final: 0.3582 (pt) REVERT: L 129 LEU cc_start: 0.7845 (tp) cc_final: 0.7430 (tm) REVERT: L 185 ILE cc_start: 0.7343 (mm) cc_final: 0.6997 (mt) REVERT: L 194 ASP cc_start: 0.7764 (p0) cc_final: 0.7270 (p0) REVERT: L 205 ARG cc_start: 0.7761 (tpt170) cc_final: 0.7487 (mmm160) REVERT: L 262 MET cc_start: 0.6270 (mmm) cc_final: 0.5696 (mmm) outliers start: 5 outliers final: 1 residues processed: 272 average time/residue: 0.6245 time to fit residues: 182.0670 Evaluate side-chains 225 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain L residue 55 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** L 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.139328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.113430 restraints weight = 28780.907| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.28 r_work: 0.3396 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14925 Z= 0.189 Angle : 0.881 17.168 21385 Z= 0.491 Chirality : 0.059 0.276 2429 Planarity : 0.006 0.061 1708 Dihedral : 30.517 168.822 4323 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.03 % Allowed : 13.30 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.25), residues: 1009 helix: 1.44 (0.20), residues: 624 sheet: -0.57 (0.86), residues: 30 loop : -1.15 (0.28), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 90 TYR 0.012 0.002 TYR B 51 PHE 0.028 0.002 PHE L 49 TRP 0.034 0.005 TRP L 276 HIS 0.006 0.001 HIS L 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.19 (14921) covalent geometry : angle 0.86572 / 0.49 (21379) hydrogen bonds : bond 0.06144 / 4.20 ( 809) hydrogen bonds : angle 3.50154 / 2.56 ( 2043) metal coordination : bond 0.01083 / 0.56 ( 4) metal coordination : angle 9.77965 / 5.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8083 (mmp) cc_final: 0.7754 (mmp) REVERT: A 105 GLU cc_start: 0.8069 (tt0) cc_final: 0.7784 (mt-10) REVERT: A 120 MET cc_start: 0.7765 (mtp) cc_final: 0.7538 (mtt) REVERT: E 59 GLU cc_start: 0.8568 (pm20) cc_final: 0.8104 (pm20) REVERT: F 35 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7832 (mtp85) REVERT: H 75 SER cc_start: 0.8812 (t) cc_final: 0.8596 (t) REVERT: H 76 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7436 (mtp85) REVERT: H 96 ARG cc_start: 0.8734 (tpp80) cc_final: 0.8350 (mtt-85) REVERT: L 49 PHE cc_start: 0.7879 (m-80) cc_final: 0.7666 (m-80) REVERT: L 95 HIS cc_start: 0.6962 (m-70) cc_final: 0.6583 (m-70) REVERT: L 114 ASN cc_start: 0.7277 (t0) cc_final: 0.6768 (m-40) REVERT: L 115 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.7485 (t) REVERT: L 136 MET cc_start: 0.7260 (mmm) cc_final: 0.6944 (mmm) REVERT: L 180 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6061 (pt0) REVERT: L 205 ARG cc_start: 0.8097 (tpt170) cc_final: 0.7735 (mmm160) REVERT: L 249 HIS cc_start: 0.6743 (OUTLIER) cc_final: 0.6512 (t-90) REVERT: L 254 ILE cc_start: 0.8525 (mm) cc_final: 0.8232 (mp) REVERT: L 262 MET cc_start: 0.7088 (mmm) cc_final: 0.6331 (mmm) outliers start: 26 outliers final: 9 residues processed: 234 average time/residue: 0.6130 time to fit residues: 154.1488 Evaluate side-chains 208 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 180 GLU Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 249 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 94 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN E 76 GLN L 95 HIS L 268 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.134242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108444 restraints weight = 28677.005| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.28 r_work: 0.3318 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 14925 Z= 0.272 Angle : 0.865 22.239 21385 Z= 0.468 Chirality : 0.058 0.319 2429 Planarity : 0.007 0.076 1708 Dihedral : 31.048 177.368 4320 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.50 % Allowed : 16.10 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.26), residues: 1009 helix: 1.52 (0.21), residues: 623 sheet: -0.79 (0.87), residues: 32 loop : -1.40 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 182 TYR 0.013 0.002 TYR G 57 PHE 0.022 0.002 PHE L 109 TRP 0.017 0.003 TRP L 276 HIS 0.006 0.001 HIS L 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.27 (14921) covalent geometry : angle 0.84116 / 0.47 (21379) hydrogen bonds : bond 0.06713 / 4.65 ( 809) hydrogen bonds : angle 3.50477 / 2.54 ( 2043) metal coordination : bond 0.01958 / 1.12 ( 4) metal coordination : angle 12.10891 / 6.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8140 (tt0) cc_final: 0.7841 (mt-10) REVERT: C 20 ARG cc_start: 0.8827 (ttm-80) cc_final: 0.8609 (ttm-80) REVERT: C 56 GLU cc_start: 0.8639 (tt0) cc_final: 0.8409 (tt0) REVERT: E 56 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8939 (ttmp) REVERT: E 105 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7755 (tm-30) REVERT: F 35 ARG cc_start: 0.8342 (mtp85) cc_final: 0.8023 (mtp85) REVERT: G 73 ASN cc_start: 0.8603 (t0) cc_final: 0.7974 (t0) REVERT: H 75 SER cc_start: 0.8890 (t) cc_final: 0.8660 (t) REVERT: H 76 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7480 (mtp85) REVERT: H 90 GLU cc_start: 0.8487 (mp0) cc_final: 0.8243 (mp0) REVERT: L 49 PHE cc_start: 0.7851 (m-80) cc_final: 0.7597 (m-80) REVERT: L 101 LEU cc_start: 0.8288 (mt) cc_final: 0.8081 (pp) REVERT: L 109 PHE cc_start: 0.6756 (t80) cc_final: 0.6475 (t80) REVERT: L 136 MET cc_start: 0.7742 (mmm) cc_final: 0.7511 (mmm) REVERT: L 194 ASP cc_start: 0.8002 (p0) cc_final: 0.7197 (p0) REVERT: L 205 ARG cc_start: 0.8166 (tpt170) cc_final: 0.7733 (mmm160) REVERT: L 262 MET cc_start: 0.7159 (mmm) cc_final: 0.6383 (mmm) REVERT: L 277 ASP cc_start: 0.8209 (p0) cc_final: 0.7706 (p0) REVERT: L 282 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7508 (pp) outliers start: 30 outliers final: 17 residues processed: 229 average time/residue: 0.5862 time to fit residues: 144.5973 Evaluate side-chains 230 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 180 GLU Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 253 ARG Chi-restraints excluded: chain L residue 271 LEU Chi-restraints excluded: chain L residue 282 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 91 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 10.9990 chunk 59 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN C 73 ASN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.135774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.110100 restraints weight = 29119.127| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.35 r_work: 0.3341 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14925 Z= 0.192 Angle : 0.763 16.219 21385 Z= 0.420 Chirality : 0.052 0.274 2429 Planarity : 0.005 0.051 1708 Dihedral : 30.883 174.412 4320 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.62 % Allowed : 18.55 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1009 helix: 1.70 (0.20), residues: 626 sheet: -0.70 (0.97), residues: 32 loop : -1.36 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 95 TYR 0.011 0.001 TYR H 80 PHE 0.022 0.001 PHE L 109 TRP 0.021 0.003 TRP L 42 HIS 0.004 0.001 HIS L 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (14921) covalent geometry : angle 0.74597 / 0.42 (21379) hydrogen bonds : bond 0.05268 / 3.59 ( 809) hydrogen bonds : angle 3.27804 / 2.38 ( 2043) metal coordination : bond 0.01342 / 0.73 ( 4) metal coordination : angle 9.50464 / 5.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 219 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8215 (m-30) cc_final: 0.7932 (m-30) REVERT: A 105 GLU cc_start: 0.8088 (tt0) cc_final: 0.7788 (mt-10) REVERT: E 105 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7737 (tm-30) REVERT: F 35 ARG cc_start: 0.8261 (mtp85) cc_final: 0.7971 (mtp85) REVERT: G 73 ASN cc_start: 0.8553 (t0) cc_final: 0.7959 (t0) REVERT: G 77 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8426 (mtm-85) REVERT: H 75 SER cc_start: 0.8858 (t) cc_final: 0.8628 (t) REVERT: H 76 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7393 (mtp85) REVERT: L 189 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7969 (tp30) REVERT: L 205 ARG cc_start: 0.8193 (tpt170) cc_final: 0.7744 (mmm160) REVERT: L 249 HIS cc_start: 0.6679 (OUTLIER) cc_final: 0.6435 (t-90) REVERT: L 262 MET cc_start: 0.7117 (mmm) cc_final: 0.6331 (mmm) REVERT: L 277 ASP cc_start: 0.8369 (p0) cc_final: 0.7827 (p0) outliers start: 31 outliers final: 16 residues processed: 231 average time/residue: 0.6080 time to fit residues: 151.2040 Evaluate side-chains 230 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 249 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 67 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.136144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110453 restraints weight = 29072.734| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.34 r_work: 0.3348 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14925 Z= 0.166 Angle : 0.725 15.297 21385 Z= 0.403 Chirality : 0.050 0.280 2429 Planarity : 0.005 0.053 1708 Dihedral : 30.652 172.051 4320 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.90 % Allowed : 19.02 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.02 (0.26), residues: 1009 helix: 1.84 (0.21), residues: 626 sheet: -0.73 (0.89), residues: 30 loop : -1.38 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 95 TYR 0.012 0.001 TYR H 80 PHE 0.009 0.001 PHE E 67 TRP 0.014 0.002 TRP L 42 HIS 0.005 0.001 HIS L 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (14921) covalent geometry : angle 0.70851 / 0.40 (21379) hydrogen bonds : bond 0.04981 / 3.38 ( 809) hydrogen bonds : angle 3.15299 / 2.28 ( 2043) metal coordination : bond 0.01260 / 0.70 ( 4) metal coordination : angle 9.13846 / 4.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 217 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8090 (tt0) cc_final: 0.7818 (tt0) REVERT: A 129 ARG cc_start: 0.8209 (ttp80) cc_final: 0.7576 (tpt90) REVERT: C 56 GLU cc_start: 0.8574 (tt0) cc_final: 0.8305 (tt0) REVERT: E 105 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7730 (tm-30) REVERT: F 35 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7940 (mtp85) REVERT: G 73 ASN cc_start: 0.8579 (t0) cc_final: 0.7998 (t0) REVERT: H 75 SER cc_start: 0.8857 (t) cc_final: 0.8629 (t) REVERT: H 76 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7375 (mtp85) REVERT: L 49 PHE cc_start: 0.7907 (m-80) cc_final: 0.7570 (t80) REVERT: L 100 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.7091 (tp-100) REVERT: L 189 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7733 (tp30) REVERT: L 194 ASP cc_start: 0.8036 (p0) cc_final: 0.6997 (p0) REVERT: L 205 ARG cc_start: 0.8166 (tpt170) cc_final: 0.7772 (mmm160) REVERT: L 277 ASP cc_start: 0.8443 (p0) cc_final: 0.7965 (p0) outliers start: 42 outliers final: 24 residues processed: 230 average time/residue: 0.6293 time to fit residues: 155.8598 Evaluate side-chains 238 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 124 PHE Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 282 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.137669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.111883 restraints weight = 29122.093| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.35 r_work: 0.3371 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14925 Z= 0.149 Angle : 0.694 13.688 21385 Z= 0.392 Chirality : 0.048 0.277 2429 Planarity : 0.005 0.059 1708 Dihedral : 30.431 170.573 4320 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.43 % Allowed : 20.19 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.21 (0.26), residues: 1009 helix: 1.98 (0.21), residues: 626 sheet: -0.47 (0.91), residues: 30 loop : -1.31 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 39 TYR 0.013 0.001 TYR H 80 PHE 0.009 0.001 PHE E 67 TRP 0.023 0.004 TRP L 42 HIS 0.004 0.001 HIS L 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (14921) covalent geometry : angle 0.68138 / 0.39 (21379) hydrogen bonds : bond 0.04621 / 3.13 ( 809) hydrogen bonds : angle 3.08434 / 2.24 ( 2043) metal coordination : bond 0.01170 / 0.66 ( 4) metal coordination : angle 7.95136 / 4.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8043 (tt0) cc_final: 0.7770 (tt0) REVERT: A 129 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7526 (tpt90) REVERT: E 105 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7736 (tm-30) REVERT: F 35 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7894 (mtp85) REVERT: F 77 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8764 (mtmp) REVERT: G 73 ASN cc_start: 0.8589 (t0) cc_final: 0.8037 (t0) REVERT: H 75 SER cc_start: 0.8840 (t) cc_final: 0.8627 (t) REVERT: H 76 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7352 (mtp85) REVERT: L 49 PHE cc_start: 0.7869 (m-80) cc_final: 0.7433 (t80) REVERT: L 101 LEU cc_start: 0.8467 (mt) cc_final: 0.8230 (mm) REVERT: L 157 MET cc_start: 0.6737 (pmm) cc_final: 0.6355 (mpp) REVERT: L 189 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7787 (tp30) REVERT: L 194 ASP cc_start: 0.7915 (p0) cc_final: 0.7214 (p0) REVERT: L 195 ARG cc_start: 0.7672 (mmm160) cc_final: 0.7429 (mmm160) REVERT: L 205 ARG cc_start: 0.8147 (tpt170) cc_final: 0.7731 (mmm160) REVERT: L 249 HIS cc_start: 0.6851 (OUTLIER) cc_final: 0.6608 (t-90) REVERT: L 277 ASP cc_start: 0.8519 (p0) cc_final: 0.7885 (p0) outliers start: 38 outliers final: 20 residues processed: 225 average time/residue: 0.6271 time to fit residues: 151.9221 Evaluate side-chains 229 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 124 PHE Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 249 HIS Chi-restraints excluded: chain L residue 282 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 77 optimal weight: 10.0000 chunk 74 optimal weight: 40.0000 chunk 119 optimal weight: 0.0870 chunk 58 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 118 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 76 GLN G 89 ASN L 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.139731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.114026 restraints weight = 28879.861| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.33 r_work: 0.3412 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14925 Z= 0.133 Angle : 0.686 13.493 21385 Z= 0.384 Chirality : 0.046 0.274 2429 Planarity : 0.005 0.078 1708 Dihedral : 30.168 171.199 4320 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.85 % Allowed : 21.24 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.31 (0.26), residues: 1009 helix: 2.10 (0.21), residues: 625 sheet: -1.35 (1.05), residues: 24 loop : -1.26 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 253 TYR 0.018 0.001 TYR D 37 PHE 0.009 0.001 PHE L 124 TRP 0.028 0.003 TRP L 42 HIS 0.005 0.001 HIS L 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.13 (14921) covalent geometry : angle 0.67519 / 0.38 (21379) hydrogen bonds : bond 0.04276 / 2.89 ( 809) hydrogen bonds : angle 3.03407 / 2.21 ( 2043) metal coordination : bond 0.00982 / 0.54 ( 4) metal coordination : angle 7.16517 / 3.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8030 (tt0) cc_final: 0.7737 (tt0) REVERT: A 129 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7636 (tpt90) REVERT: C 56 GLU cc_start: 0.8497 (tt0) cc_final: 0.8226 (tt0) REVERT: C 99 ARG cc_start: 0.8342 (mmm-85) cc_final: 0.8008 (mmm-85) REVERT: E 105 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7681 (tm-30) REVERT: F 35 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7855 (mtp85) REVERT: G 73 ASN cc_start: 0.8585 (t0) cc_final: 0.8065 (t0) REVERT: H 75 SER cc_start: 0.8855 (t) cc_final: 0.8637 (t) REVERT: H 76 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7314 (mtp85) REVERT: L 49 PHE cc_start: 0.7704 (m-80) cc_final: 0.7411 (t80) REVERT: L 153 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7959 (p) REVERT: L 189 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7583 (tp30) REVERT: L 194 ASP cc_start: 0.7962 (p0) cc_final: 0.7128 (p0) REVERT: L 205 ARG cc_start: 0.8077 (tpt170) cc_final: 0.7692 (mmm160) REVERT: L 249 HIS cc_start: 0.6880 (OUTLIER) cc_final: 0.6596 (t-90) REVERT: L 277 ASP cc_start: 0.8439 (p0) cc_final: 0.7880 (p0) outliers start: 33 outliers final: 18 residues processed: 227 average time/residue: 0.6392 time to fit residues: 156.2856 Evaluate side-chains 228 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 124 PHE Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 249 HIS Chi-restraints excluded: chain L residue 266 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 102 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.139838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114177 restraints weight = 28949.281| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.34 r_work: 0.3413 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14925 Z= 0.142 Angle : 0.675 11.264 21385 Z= 0.381 Chirality : 0.045 0.287 2429 Planarity : 0.005 0.073 1708 Dihedral : 30.031 172.600 4320 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.50 % Allowed : 22.29 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.38 (0.27), residues: 1009 helix: 2.14 (0.21), residues: 629 sheet: -0.81 (0.93), residues: 32 loop : -1.28 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 30 TYR 0.019 0.001 TYR H 80 PHE 0.008 0.001 PHE E 67 TRP 0.027 0.003 TRP L 42 HIS 0.007 0.001 HIS L 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (14921) covalent geometry : angle 0.66367 / 0.38 (21379) hydrogen bonds : bond 0.04272 / 2.90 ( 809) hydrogen bonds : angle 3.02376 / 2.20 ( 2043) metal coordination : bond 0.01036 / 0.62 ( 4) metal coordination : angle 7.31903 / 4.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8045 (tt0) cc_final: 0.7745 (tt0) REVERT: A 129 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7629 (tpt90) REVERT: C 56 GLU cc_start: 0.8464 (tt0) cc_final: 0.8183 (tt0) REVERT: F 35 ARG cc_start: 0.8199 (mtp85) cc_final: 0.7869 (mtp85) REVERT: F 77 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8791 (mtmp) REVERT: G 73 ASN cc_start: 0.8596 (t0) cc_final: 0.8084 (t0) REVERT: H 75 SER cc_start: 0.8863 (t) cc_final: 0.8643 (t) REVERT: H 76 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7320 (mtp85) REVERT: L 49 PHE cc_start: 0.7788 (m-80) cc_final: 0.7367 (t80) REVERT: L 157 MET cc_start: 0.6600 (pmm) cc_final: 0.6345 (mpp) REVERT: L 194 ASP cc_start: 0.7934 (p0) cc_final: 0.7493 (p0) REVERT: L 205 ARG cc_start: 0.8084 (tpt170) cc_final: 0.7716 (mmm160) REVERT: L 249 HIS cc_start: 0.6945 (OUTLIER) cc_final: 0.6639 (t-90) REVERT: L 282 LEU cc_start: 0.7843 (mt) cc_final: 0.7612 (pp) outliers start: 30 outliers final: 18 residues processed: 224 average time/residue: 0.6245 time to fit residues: 150.9691 Evaluate side-chains 227 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 124 PHE Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 249 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 56 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 0.0370 chunk 46 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 76 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.140925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.115186 restraints weight = 29318.611| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.37 r_work: 0.3430 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 14925 Z= 0.138 Angle : 0.674 11.598 21385 Z= 0.380 Chirality : 0.045 0.288 2429 Planarity : 0.005 0.053 1708 Dihedral : 29.900 174.878 4320 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.50 % Allowed : 22.64 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.40 (0.26), residues: 1009 helix: 2.19 (0.20), residues: 629 sheet: -1.08 (0.91), residues: 30 loop : -1.32 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 253 TYR 0.020 0.001 TYR D 37 PHE 0.008 0.001 PHE L 49 TRP 0.031 0.003 TRP L 42 HIS 0.004 0.001 HIS L 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (14921) covalent geometry : angle 0.66343 / 0.38 (21379) hydrogen bonds : bond 0.04172 / 2.83 ( 809) hydrogen bonds : angle 3.00002 / 2.19 ( 2043) metal coordination : bond 0.01084 / 0.65 ( 4) metal coordination : angle 7.17639 / 3.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8033 (tt0) cc_final: 0.7733 (tt0) REVERT: A 129 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7620 (tpt90) REVERT: C 56 GLU cc_start: 0.8552 (tt0) cc_final: 0.8272 (tt0) REVERT: E 105 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7651 (tm-30) REVERT: F 35 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7946 (mtp85) REVERT: F 77 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8788 (mtmp) REVERT: G 73 ASN cc_start: 0.8591 (t0) cc_final: 0.8087 (t0) REVERT: H 75 SER cc_start: 0.8887 (t) cc_final: 0.8674 (t) REVERT: H 76 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7371 (mtp85) REVERT: L 49 PHE cc_start: 0.7664 (m-80) cc_final: 0.7352 (t80) REVERT: L 194 ASP cc_start: 0.7909 (p0) cc_final: 0.7392 (p0) REVERT: L 205 ARG cc_start: 0.8024 (tpt170) cc_final: 0.7662 (mmm160) REVERT: L 249 HIS cc_start: 0.7018 (OUTLIER) cc_final: 0.6793 (t70) outliers start: 30 outliers final: 22 residues processed: 225 average time/residue: 0.6018 time to fit residues: 145.9759 Evaluate side-chains 225 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 124 PHE Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 249 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 85 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.136311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110327 restraints weight = 28751.882| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.35 r_work: 0.3348 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14925 Z= 0.217 Angle : 0.771 19.213 21385 Z= 0.416 Chirality : 0.049 0.333 2429 Planarity : 0.006 0.059 1708 Dihedral : 29.888 175.635 4320 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.68 % Allowed : 24.15 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.12 (0.26), residues: 1009 helix: 1.97 (0.21), residues: 630 sheet: -1.03 (0.94), residues: 30 loop : -1.47 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 182 TYR 0.024 0.002 TYR D 37 PHE 0.013 0.002 PHE L 109 TRP 0.029 0.003 TRP L 42 HIS 0.006 0.001 HIS L 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (14921) covalent geometry : angle 0.74969 / 0.41 (21379) hydrogen bonds : bond 0.05348 / 3.68 ( 809) hydrogen bonds : angle 3.21644 / 2.34 ( 2043) metal coordination : bond 0.01534 / 0.90 ( 4) metal coordination : angle 10.70632 / 5.68 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8080 (tt0) cc_final: 0.7812 (tt0) REVERT: A 129 ARG cc_start: 0.8125 (ttp80) cc_final: 0.7553 (tpt90) REVERT: F 35 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7944 (mtp85) REVERT: G 73 ASN cc_start: 0.8653 (t0) cc_final: 0.8102 (t0) REVERT: H 75 SER cc_start: 0.8914 (t) cc_final: 0.8705 (t) REVERT: H 76 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7406 (mtp85) REVERT: L 49 PHE cc_start: 0.7793 (m-80) cc_final: 0.7528 (t80) REVERT: L 153 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8188 (t) REVERT: L 194 ASP cc_start: 0.7949 (p0) cc_final: 0.7567 (p0) REVERT: L 205 ARG cc_start: 0.8160 (tpt170) cc_final: 0.7696 (mmm160) REVERT: L 249 HIS cc_start: 0.7095 (OUTLIER) cc_final: 0.6836 (t70) outliers start: 23 outliers final: 17 residues processed: 216 average time/residue: 0.5840 time to fit residues: 136.2023 Evaluate side-chains 222 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 124 PHE Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 249 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 121 optimal weight: 0.0670 chunk 88 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 34 optimal weight: 0.0970 chunk 71 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 74 optimal weight: 50.0000 chunk 96 optimal weight: 10.0000 overall best weight: 1.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN L 246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.138198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.112385 restraints weight = 28800.189| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.35 r_work: 0.3379 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14925 Z= 0.157 Angle : 0.737 17.352 21385 Z= 0.400 Chirality : 0.047 0.299 2429 Planarity : 0.005 0.057 1708 Dihedral : 29.833 176.555 4320 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.57 % Allowed : 25.20 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % 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: 1.20 (0.27), residues: 1009 helix: 2.05 (0.21), residues: 626 sheet: -1.13 (0.97), residues: 30 loop : -1.40 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 20 TYR 0.024 0.002 TYR D 37 PHE 0.010 0.001 PHE L 124 TRP 0.030 0.003 TRP L 42 HIS 0.007 0.001 HIS L 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (14921) covalent geometry : angle 0.72125 / 0.40 (21379) hydrogen bonds : bond 0.04607 / 3.15 ( 809) hydrogen bonds : angle 3.13165 / 2.28 ( 2043) metal coordination : bond 0.01434 / 0.85 ( 4) metal coordination : angle 8.96228 / 4.87 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4298.20 seconds wall clock time: 73 minutes 38.45 seconds (4418.45 seconds total)