Starting phenix.real_space_refine on Thu Aug 6 04:52:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8of4_16845/08_2026/8of4_16845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8of4_16845/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8of4_16845/08_2026/8of4_16845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8of4_16845/08_2026/8of4_16845.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8of4_16845/08_2026/8of4_16845.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8of4_16845/08_2026/8of4_16845.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8of4_16845/08_2026/8of4_16845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8of4_16845/08_2026/8of4_16845.map" } 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-2.2rc3-6140/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: 2.58, per 1000 atoms: 0.18 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: 1.19 Conformation dependent library (CDL) restraints added in 483.8 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: 1.36 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: 2.31 Time building geometry restraints manager: 1.60 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.050 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.350 ------------------------------------------------------------------------------- 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 : 2.011 62.518 21385 Z= 1.976 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 1.99730 / 1.98 (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 : 0.347 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: 0.7851 (mmp) REVERT: D 59 MET cc_start: 0.8475 (mmm) cc_final: 0.8211 (mmp) REVERT: F 35 ARG cc_start: 0.7647 (mtp85) cc_final: 0.6882 (mtp85) REVERT: H 75 SER cc_start: 0.8778 (t) cc_final: 0.8542 (t) REVERT: H 96 ARG cc_start: 0.8472 (tpp80) cc_final: 0.7953 (ttt-90) REVERT: H 112 THR cc_start: 0.8798 (t) cc_final: 0.8455 (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: 0.5697 (mmm) outliers start: 5 outliers final: 1 residues processed: 272 average time/residue: 0.7322 time to fit residues: 213.8169 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 : 0.389 ------------------------------------------------------------------------------- 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 L 133 HIS 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 = 0.139488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.113589 restraints weight = 28779.631| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.28 r_work: 0.3399 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14925 Z= 0.193 Angle : 0.888 16.623 21385 Z= 0.490 Chirality : 0.061 0.285 2429 Planarity : 0.006 0.067 1708 Dihedral : 30.509 168.455 4323 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.15 % Allowed : 13.30 % Favored : 83.55 % 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: 0.78 (0.25), residues: 1009 helix: 1.47 (0.20), residues: 624 sheet: -0.53 (0.85), residues: 30 loop : -1.10 (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 0.029 0.002 PHE L 49 TRP 0.032 0.004 TRP L 276 HIS 0.007 0.001 HIS L 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.19 (14921) covalent geometry : angle 0.87380 / 0.49 (21379) hydrogen bonds : bond 0.06082 / 4.15 ( 809) hydrogen bonds : angle 3.48394 / 2.55 ( 2043) metal coordination : bond 0.00949 / 0.52 ( 4) metal coordination : angle 9.57224 / 5.08 ( 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 256 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8082 (mmp) cc_final: 0.7757 (mmp) REVERT: A 105 GLU cc_start: 0.8075 (tt0) cc_final: 0.7787 (mt-10) REVERT: F 35 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7827 (mtp85) REVERT: H 75 SER cc_start: 0.8811 (t) cc_final: 0.8594 (t) REVERT: H 76 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7460 (mtp85) REVERT: H 85 THR cc_start: 0.8875 (m) cc_final: 0.8640 (t) REVERT: H 96 ARG cc_start: 0.8736 (tpp80) cc_final: 0.8359 (mtt-85) REVERT: L 95 HIS cc_start: 0.6973 (m-70) cc_final: 0.6592 (m-70) REVERT: L 114 ASN cc_start: 0.7270 (t0) cc_final: 0.6751 (m-40) REVERT: L 115 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.7448 (t) REVERT: L 136 MET cc_start: 0.7314 (mmm) cc_final: 0.6918 (mmm) REVERT: L 205 ARG cc_start: 0.8094 (tpt170) cc_final: 0.7731 (mmm160) REVERT: L 249 HIS cc_start: 0.6683 (OUTLIER) cc_final: 0.6458 (t-90) REVERT: L 254 ILE cc_start: 0.8544 (mm) cc_final: 0.8249 (mp) REVERT: L 262 MET cc_start: 0.7097 (mmm) cc_final: 0.6336 (mmm) outliers start: 27 outliers final: 10 residues processed: 240 average time/residue: 0.6870 time to fit residues: 177.1991 Evaluate side-chains 216 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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: 0.0370 chunk 64 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.136167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110459 restraints weight = 29197.448| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.34 r_work: 0.3345 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14925 Z= 0.196 Angle : 0.819 18.696 21385 Z= 0.446 Chirality : 0.057 0.374 2429 Planarity : 0.006 0.055 1708 Dihedral : 30.942 177.304 4320 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.62 % Allowed : 15.75 % Favored : 80.63 % 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: 1.04 (0.26), residues: 1009 helix: 1.78 (0.21), residues: 623 sheet: -0.13 (0.89), residues: 31 loop : -1.25 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 95 TYR 0.014 0.002 TYR H 80 PHE 0.018 0.002 PHE L 109 TRP 0.016 0.003 TRP L 276 HIS 0.008 0.001 HIS L 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.20 (14921) covalent geometry : angle 0.79941 / 0.45 (21379) hydrogen bonds : bond 0.05972 / 4.10 ( 809) hydrogen bonds : angle 3.34279 / 2.43 ( 2043) metal coordination : bond 0.01263 / 0.66 ( 4) metal coordination : angle 10.58284 / 5.62 ( 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 252 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8056 (mmp) cc_final: 0.7774 (mmp) REVERT: A 105 GLU cc_start: 0.8109 (tt0) cc_final: 0.7791 (mt-10) REVERT: E 105 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7747 (tm-30) REVERT: F 35 ARG cc_start: 0.8280 (mtp85) cc_final: 0.7955 (mtp85) REVERT: F 85 ASP cc_start: 0.8340 (m-30) cc_final: 0.8135 (m-30) REVERT: G 73 ASN cc_start: 0.8526 (t0) cc_final: 0.7926 (t0) REVERT: H 75 SER cc_start: 0.8786 (t) cc_final: 0.8538 (t) REVERT: H 76 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7376 (mtp85) REVERT: L 49 PHE cc_start: 0.8047 (m-80) cc_final: 0.7602 (t80) REVERT: L 95 HIS cc_start: 0.6955 (m90) cc_final: 0.6662 (m90) REVERT: L 100 GLN cc_start: 0.7955 (tp-100) cc_final: 0.7537 (tp-100) REVERT: L 109 PHE cc_start: 0.6715 (t80) cc_final: 0.6295 (t80) REVERT: L 136 MET cc_start: 0.7590 (mmm) cc_final: 0.7368 (mmm) REVERT: L 194 ASP cc_start: 0.8096 (p0) cc_final: 0.7037 (p0) REVERT: L 205 ARG cc_start: 0.8177 (tpt170) cc_final: 0.7763 (mmm160) REVERT: L 249 HIS cc_start: 0.6903 (OUTLIER) cc_final: 0.6699 (t-90) REVERT: L 262 MET cc_start: 0.7171 (mmm) cc_final: 0.6356 (mmm) REVERT: L 277 ASP cc_start: 0.8293 (p0) cc_final: 0.7774 (p0) outliers start: 31 outliers final: 16 residues processed: 232 average time/residue: 0.7505 time to fit residues: 186.8060 Evaluate side-chains 227 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 57 SER 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 149 VAL Chi-restraints excluded: chain L residue 180 GLU Chi-restraints excluded: chain L residue 211 ILE Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 249 HIS 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: 6.9990 chunk 76 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 10.9990 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.136271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.110495 restraints weight = 28513.173| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.39 r_work: 0.3338 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14925 Z= 0.211 Angle : 0.790 16.507 21385 Z= 0.429 Chirality : 0.053 0.311 2429 Planarity : 0.005 0.054 1708 Dihedral : 30.734 174.969 4320 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.32 % Allowed : 17.97 % Favored : 77.71 % 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: 1.00 (0.26), residues: 1009 helix: 1.81 (0.21), residues: 625 sheet: -0.50 (1.17), residues: 22 loop : -1.37 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 95 TYR 0.015 0.002 TYR H 80 PHE 0.015 0.001 PHE L 49 TRP 0.020 0.003 TRP L 42 HIS 0.007 0.001 HIS L 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.21 (14921) covalent geometry : angle 0.77234 / 0.43 (21379) hydrogen bonds : bond 0.05406 / 3.69 ( 809) hydrogen bonds : angle 3.19036 / 2.32 ( 2043) metal coordination : bond 0.01382 / 0.77 ( 4) metal coordination : angle 9.88627 / 5.37 ( 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 246 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8129 (tt0) cc_final: 0.7863 (tt0) REVERT: C 29 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8384 (ttm170) REVERT: E 42 ARG cc_start: 0.6417 (mpp-170) cc_final: 0.6182 (mpp-170) REVERT: E 105 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7778 (tm-30) REVERT: F 35 ARG cc_start: 0.8312 (mtp85) cc_final: 0.8080 (mtp85) REVERT: F 85 ASP cc_start: 0.8327 (m-30) cc_final: 0.8095 (m-30) REVERT: G 73 ASN cc_start: 0.8548 (t0) cc_final: 0.7970 (t0) REVERT: H 75 SER cc_start: 0.8857 (t) cc_final: 0.8623 (t) REVERT: H 76 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7470 (mtp85) REVERT: L 49 PHE cc_start: 0.8042 (m-80) cc_final: 0.7595 (t80) REVERT: L 136 MET cc_start: 0.7752 (mmm) cc_final: 0.7412 (mmm) REVERT: L 189 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8054 (tp30) REVERT: L 194 ASP cc_start: 0.8094 (p0) cc_final: 0.7147 (p0) REVERT: L 205 ARG cc_start: 0.8222 (tpt170) cc_final: 0.7757 (mmm160) REVERT: L 249 HIS cc_start: 0.6887 (OUTLIER) cc_final: 0.6661 (t-90) REVERT: L 262 MET cc_start: 0.7129 (mmm) cc_final: 0.6364 (mmm) REVERT: L 277 ASP cc_start: 0.8425 (p0) cc_final: 0.7950 (p0) outliers start: 37 outliers final: 22 residues processed: 224 average time/residue: 0.7050 time to fit residues: 169.9052 Evaluate side-chains 232 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 29 ARG 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 85 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 94 GLU 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 115 VAL 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 211 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 67 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 0.0060 chunk 14 optimal weight: 0.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.137886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.112142 restraints weight = 29044.575| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.35 r_work: 0.3375 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14925 Z= 0.147 Angle : 0.715 16.072 21385 Z= 0.397 Chirality : 0.049 0.299 2429 Planarity : 0.005 0.046 1708 Dihedral : 30.448 171.533 4320 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.27 % Allowed : 19.84 % Favored : 76.90 % 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: 1.19 (0.26), residues: 1009 helix: 1.95 (0.21), residues: 627 sheet: -0.74 (0.91), residues: 30 loop : -1.27 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 20 TYR 0.013 0.001 TYR H 80 PHE 0.011 0.001 PHE L 49 TRP 0.021 0.003 TRP L 42 HIS 0.003 0.001 HIS L 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (14921) covalent geometry : angle 0.69985 / 0.40 (21379) hydrogen bonds : bond 0.04754 / 3.22 ( 809) hydrogen bonds : angle 3.10044 / 2.26 ( 2043) metal coordination : bond 0.01113 / 0.67 ( 4) metal coordination : angle 8.64722 / 4.80 ( 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 242 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8064 (tt0) cc_final: 0.7747 (mt-10) REVERT: A 129 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7512 (tpt90) REVERT: E 105 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7707 (tm-30) REVERT: F 35 ARG cc_start: 0.8221 (mtp85) cc_final: 0.7999 (mtp85) REVERT: F 85 ASP cc_start: 0.8239 (m-30) cc_final: 0.7967 (m-30) REVERT: G 73 ASN cc_start: 0.8553 (t0) cc_final: 0.7992 (t0) REVERT: H 75 SER cc_start: 0.8810 (t) cc_final: 0.8580 (t) REVERT: H 76 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7352 (mtp85) REVERT: L 49 PHE cc_start: 0.7917 (m-80) cc_final: 0.7597 (t80) REVERT: L 109 PHE cc_start: 0.6247 (t80) cc_final: 0.5934 (t80) REVERT: L 180 GLU cc_start: 0.7141 (tt0) cc_final: 0.6599 (tt0) REVERT: L 182 ARG cc_start: 0.5787 (tpp80) cc_final: 0.5233 (tpp80) REVERT: L 194 ASP cc_start: 0.8065 (p0) cc_final: 0.7534 (p0) REVERT: L 205 ARG cc_start: 0.8137 (tpt170) cc_final: 0.7667 (mmm160) REVERT: L 249 HIS cc_start: 0.7003 (OUTLIER) cc_final: 0.6747 (t-90) REVERT: L 269 LEU cc_start: 0.6319 (OUTLIER) cc_final: 0.5373 (pp) REVERT: L 277 ASP cc_start: 0.8588 (p0) cc_final: 0.7975 (p0) REVERT: L 282 LEU cc_start: 0.7882 (mt) cc_final: 0.7452 (pp) outliers start: 28 outliers final: 12 residues processed: 224 average time/residue: 0.7331 time to fit residues: 176.8180 Evaluate side-chains 222 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE 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 63 LEU Chi-restraints excluded: chain C residue 118 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 L residue 51 THR Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 211 ILE Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 249 HIS Chi-restraints excluded: chain L residue 269 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: 2.9990 chunk 19 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN G 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.136450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110611 restraints weight = 28925.245| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.35 r_work: 0.3356 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14925 Z= 0.181 Angle : 0.755 15.958 21385 Z= 0.409 Chirality : 0.050 0.321 2429 Planarity : 0.005 0.065 1708 Dihedral : 30.298 171.025 4320 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.43 % Allowed : 19.72 % Favored : 75.85 % 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: 1.17 (0.26), residues: 1009 helix: 1.96 (0.21), residues: 627 sheet: -1.18 (0.90), residues: 32 loop : -1.28 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 20 TYR 0.019 0.002 TYR H 80 PHE 0.022 0.002 PHE L 109 TRP 0.022 0.003 TRP L 42 HIS 0.003 0.001 HIS L 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 (14921) covalent geometry : angle 0.73897 / 0.41 (21379) hydrogen bonds : bond 0.05012 / 3.43 ( 809) hydrogen bonds : angle 3.11518 / 2.26 ( 2043) metal coordination : bond 0.01495 / 0.90 ( 4) metal coordination : angle 9.27080 / 4.94 ( 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 242 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8049 (tt0) cc_final: 0.7787 (tt0) REVERT: B 93 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7937 (mp10) REVERT: E 105 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7750 (tm-30) REVERT: F 35 ARG cc_start: 0.8269 (mtp85) cc_final: 0.8048 (mtp85) REVERT: F 77 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8782 (mtmp) REVERT: F 85 ASP cc_start: 0.8264 (m-30) cc_final: 0.7980 (m-30) REVERT: G 73 ASN cc_start: 0.8587 (t0) cc_final: 0.8018 (t0) REVERT: H 75 SER cc_start: 0.8849 (t) cc_final: 0.8611 (t) REVERT: H 76 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7375 (mtp85) REVERT: L 180 GLU cc_start: 0.7000 (tt0) cc_final: 0.6542 (tt0) REVERT: L 182 ARG cc_start: 0.5763 (tpp80) cc_final: 0.5174 (tpp80) REVERT: L 194 ASP cc_start: 0.8073 (p0) cc_final: 0.7681 (p0) REVERT: L 205 ARG cc_start: 0.8186 (tpt170) cc_final: 0.7764 (mmm160) REVERT: L 249 HIS cc_start: 0.6978 (OUTLIER) cc_final: 0.6701 (t-90) REVERT: L 277 ASP cc_start: 0.8556 (p0) cc_final: 0.7931 (p0) outliers start: 38 outliers final: 24 residues processed: 222 average time/residue: 0.7483 time to fit residues: 179.0239 Evaluate side-chains 225 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 63 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 63 LEU 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 E residue 57 SER Chi-restraints excluded: chain F residue 77 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 51 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain L residue 211 ILE 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: 9.9990 chunk 74 optimal weight: 40.0000 chunk 119 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.137096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.111225 restraints weight = 28756.834| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.34 r_work: 0.3363 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14925 Z= 0.164 Angle : 0.719 14.153 21385 Z= 0.396 Chirality : 0.048 0.309 2429 Planarity : 0.005 0.050 1708 Dihedral : 30.077 170.582 4320 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.62 % Allowed : 21.00 % 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: 1.24 (0.26), residues: 1009 helix: 2.02 (0.21), residues: 627 sheet: -0.88 (0.93), residues: 32 loop : -1.30 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 20 TYR 0.016 0.001 TYR H 80 PHE 0.018 0.002 PHE L 124 TRP 0.026 0.003 TRP L 42 HIS 0.006 0.001 HIS L 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (14921) covalent geometry : angle 0.70383 / 0.39 (21379) hydrogen bonds : bond 0.04739 / 3.23 ( 809) hydrogen bonds : angle 3.08332 / 2.25 ( 2043) metal coordination : bond 0.01432 / 0.85 ( 4) metal coordination : angle 8.75804 / 4.74 ( 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 241 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8026 (tt0) cc_final: 0.7751 (tt0) REVERT: A 129 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7539 (tpt90) REVERT: B 93 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7893 (mp10) REVERT: E 105 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7699 (tm-30) REVERT: F 35 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7354 (mtp85) REVERT: F 77 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8769 (mtmp) REVERT: F 85 ASP cc_start: 0.8327 (m-30) cc_final: 0.8033 (m-30) REVERT: G 73 ASN cc_start: 0.8593 (t0) cc_final: 0.8037 (t0) REVERT: H 75 SER cc_start: 0.8826 (t) cc_final: 0.8599 (t) REVERT: H 76 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7375 (mtp85) REVERT: L 49 PHE cc_start: 0.7762 (m-80) cc_final: 0.7430 (t80) REVERT: L 95 HIS cc_start: 0.7120 (m90) cc_final: 0.6837 (m90) REVERT: L 100 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.7091 (tt0) REVERT: L 194 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7640 (p0) REVERT: L 205 ARG cc_start: 0.8182 (tpt170) cc_final: 0.7735 (mmm160) REVERT: L 249 HIS cc_start: 0.7000 (t-90) cc_final: 0.6707 (t-90) REVERT: L 277 ASP cc_start: 0.8537 (p0) cc_final: 0.8075 (p0) REVERT: L 282 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7522 (pp) outliers start: 31 outliers final: 17 residues processed: 222 average time/residue: 0.7454 time to fit residues: 178.0791 Evaluate side-chains 229 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 63 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN 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 85 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 77 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 L residue 51 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 282 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 102 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.137870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.112034 restraints weight = 28690.880| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.34 r_work: 0.3377 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14925 Z= 0.151 Angle : 0.724 16.288 21385 Z= 0.395 Chirality : 0.047 0.314 2429 Planarity : 0.005 0.068 1708 Dihedral : 29.961 171.597 4320 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.38 % Allowed : 21.94 % Favored : 74.68 % 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: 1.26 (0.26), residues: 1009 helix: 2.06 (0.21), residues: 627 sheet: -1.12 (0.93), residues: 31 loop : -1.30 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 39 TYR 0.016 0.001 TYR D 37 PHE 0.015 0.001 PHE L 49 TRP 0.027 0.003 TRP L 42 HIS 0.007 0.001 HIS L 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (14921) covalent geometry : angle 0.70978 / 0.39 (21379) hydrogen bonds : bond 0.04593 / 3.13 ( 809) hydrogen bonds : angle 3.09053 / 2.26 ( 2043) metal coordination : bond 0.01298 / 0.76 ( 4) metal coordination : angle 8.47047 / 4.60 ( 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 236 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8018 (tt0) cc_final: 0.7748 (tt0) REVERT: A 129 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7558 (tpt90) REVERT: B 93 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: E 105 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7665 (tm-30) REVERT: F 35 ARG cc_start: 0.8214 (mtp85) cc_final: 0.7344 (mtp85) REVERT: F 77 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8798 (mtmp) REVERT: F 85 ASP cc_start: 0.8311 (m-30) cc_final: 0.7992 (m-30) REVERT: G 73 ASN cc_start: 0.8637 (t0) cc_final: 0.8100 (t0) REVERT: H 75 SER cc_start: 0.8843 (t) cc_final: 0.8614 (t) REVERT: H 76 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7379 (mtp85) REVERT: L 49 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7474 (t80) REVERT: L 95 HIS cc_start: 0.7096 (m90) cc_final: 0.6751 (m90) REVERT: L 194 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7575 (p0) REVERT: L 205 ARG cc_start: 0.8157 (tpt170) cc_final: 0.7726 (mmm160) REVERT: L 249 HIS cc_start: 0.7038 (t-90) cc_final: 0.6716 (t-90) REVERT: L 277 ASP cc_start: 0.8499 (p0) cc_final: 0.8005 (p0) REVERT: L 282 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7526 (pp) outliers start: 29 outliers final: 16 residues processed: 218 average time/residue: 0.7188 time to fit residues: 168.5404 Evaluate side-chains 227 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 93 GLN Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN 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 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 49 PHE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 211 ILE Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 282 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 56 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.138802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113000 restraints weight = 29088.641| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.36 r_work: 0.3394 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3843 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= 0.143 Angle : 0.714 14.031 21385 Z= 0.391 Chirality : 0.046 0.316 2429 Planarity : 0.005 0.058 1708 Dihedral : 29.850 173.107 4320 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.27 % Allowed : 22.40 % Favored : 74.33 % 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: 1.29 (0.26), residues: 1009 helix: 2.09 (0.21), residues: 626 sheet: -1.13 (0.93), residues: 31 loop : -1.29 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 20 TYR 0.017 0.001 TYR H 80 PHE 0.016 0.001 PHE L 49 TRP 0.031 0.003 TRP L 42 HIS 0.006 0.001 HIS L 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (14921) covalent geometry : angle 0.70194 / 0.39 (21379) hydrogen bonds : bond 0.04399 / 3.00 ( 809) hydrogen bonds : angle 3.06400 / 2.24 ( 2043) metal coordination : bond 0.01192 / 0.71 ( 4) metal coordination : angle 7.87309 / 4.31 ( 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 239 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8022 (tt0) cc_final: 0.7748 (tt0) REVERT: A 129 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7569 (tpt90) REVERT: B 93 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7886 (mp10) REVERT: F 35 ARG cc_start: 0.8221 (mtp85) cc_final: 0.7367 (mtp85) REVERT: F 77 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8784 (mtmp) REVERT: F 85 ASP cc_start: 0.8307 (m-30) cc_final: 0.7979 (m-30) REVERT: G 73 ASN cc_start: 0.8641 (t0) cc_final: 0.8106 (t0) REVERT: H 75 SER cc_start: 0.8849 (t) cc_final: 0.8623 (t) REVERT: H 76 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7378 (mtp85) REVERT: L 95 HIS cc_start: 0.7146 (m90) cc_final: 0.6780 (m90) REVERT: L 194 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7575 (p0) REVERT: L 205 ARG cc_start: 0.8157 (tpt170) cc_final: 0.7717 (mmm160) REVERT: L 249 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6909 (t-90) REVERT: L 277 ASP cc_start: 0.8366 (p0) cc_final: 0.7747 (p0) outliers start: 28 outliers final: 21 residues processed: 223 average time/residue: 0.7686 time to fit residues: 184.2816 Evaluate side-chains 231 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 63 GLU Chi-restraints excluded: chain B residue 93 GLN 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 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 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 180 GLU Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 199 LEU 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 282 LEU 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: 0.9990 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3924 r_free = 0.3924 target = 0.137824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.111938 restraints weight = 28810.954| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.34 r_work: 0.3376 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14925 Z= 0.165 Angle : 0.743 16.188 21385 Z= 0.402 Chirality : 0.047 0.333 2429 Planarity : 0.006 0.096 1708 Dihedral : 29.831 174.541 4320 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.15 % Allowed : 22.87 % Favored : 73.98 % 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: 1.23 (0.26), residues: 1009 helix: 2.06 (0.21), residues: 627 sheet: -1.46 (1.10), residues: 23 loop : -1.36 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 30 TYR 0.022 0.002 TYR D 37 PHE 0.015 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 0.00327 / 0.16 (14921) covalent geometry : angle 0.72646 / 0.40 (21379) hydrogen bonds : bond 0.04658 / 3.19 ( 809) hydrogen bonds : angle 3.09381 / 2.26 ( 2043) metal coordination : bond 0.01516 / 0.90 ( 4) metal coordination : angle 9.42553 / 5.07 ( 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 235 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8034 (tt0) cc_final: 0.7756 (tt0) REVERT: A 129 ARG cc_start: 0.8076 (ttp80) cc_final: 0.7575 (tpt90) REVERT: B 93 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: F 35 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7387 (mtp85) REVERT: F 85 ASP cc_start: 0.8291 (m-30) cc_final: 0.7962 (m-30) REVERT: G 73 ASN cc_start: 0.8643 (t0) cc_final: 0.8080 (t0) REVERT: H 75 SER cc_start: 0.8859 (t) cc_final: 0.8620 (t) REVERT: H 76 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7354 (mtp85) REVERT: L 49 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7479 (t80) REVERT: L 95 HIS cc_start: 0.7164 (m90) cc_final: 0.6791 (m90) REVERT: L 194 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7607 (p0) REVERT: L 205 ARG cc_start: 0.8168 (tpt170) cc_final: 0.7719 (mmm160) REVERT: L 249 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6922 (t-90) REVERT: L 277 ASP cc_start: 0.8320 (p0) cc_final: 0.7714 (p0) outliers start: 27 outliers final: 19 residues processed: 218 average time/residue: 0.7567 time to fit residues: 177.5324 Evaluate side-chains 230 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 93 GLN 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 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 98 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 49 PHE 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 194 ASP 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 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 121 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 122 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 34 optimal weight: 0.0060 chunk 71 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 74 optimal weight: 50.0000 chunk 96 optimal weight: 10.0000 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.139882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.114170 restraints weight = 28947.675| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.34 r_work: 0.3412 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14925 Z= 0.138 Angle : 0.712 13.641 21385 Z= 0.390 Chirality : 0.045 0.316 2429 Planarity : 0.005 0.112 1708 Dihedral : 29.745 177.145 4320 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.15 % Allowed : 23.69 % 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: 1.28 (0.27), residues: 1009 helix: 2.16 (0.21), residues: 626 sheet: -2.78 (0.82), residues: 33 loop : -1.27 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 30 TYR 0.020 0.002 TYR D 37 PHE 0.015 0.001 PHE L 49 TRP 0.030 0.003 TRP L 42 HIS 0.005 0.001 HIS L 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (14921) covalent geometry : angle 0.69892 / 0.39 (21379) hydrogen bonds : bond 0.04256 / 2.90 ( 809) hydrogen bonds : angle 3.04557 / 2.23 ( 2043) metal coordination : bond 0.01189 / 0.69 ( 4) metal coordination : angle 7.99295 / 4.39 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4971.45 seconds wall clock time: 85 minutes 16.34 seconds (5116.34 seconds total)