Starting phenix.real_space_refine on Thu Jul 31 15:44:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8of4_16845/07_2025/8of4_16845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8of4_16845/07_2025/8of4_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_2025/8of4_16845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8of4_16845/07_2025/8of4_16845.map" model { file = "/net/cci-nas-00/data/ceres_data/8of4_16845/07_2025/8of4_16845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8of4_16845/07_2025/8of4_16845.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.86, per 1000 atoms: 0.63 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: 3.35 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 6.81 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: 7.35 Time building geometry restraints manager: 4.09 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=" 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 bond pdb=" CZ ARG H 96 " pdb=" NH2 ARG H 96 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.30e-02 5.92e+03 1.29e+01 bond pdb=" CZ ARG A 72 " pdb=" NH2 ARG A 72 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.17e+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=" CA PRO E 38 " pdb=" N PRO E 38 " pdb=" CD PRO E 38 " ideal model delta sigma weight residual 112.00 100.79 11.21 1.40e+00 5.10e-01 6.41e+01 angle pdb=" CA LYS C 118 " pdb=" C LYS C 118 " pdb=" O LYS C 118 " ideal model delta sigma weight residual 121.51 112.88 8.63 1.12e+00 7.97e-01 5.94e+01 angle pdb=" C SER C 122 " pdb=" N ALA C 123 " pdb=" CA ALA C 123 " ideal model delta sigma weight residual 121.70 134.68 -12.98 1.80e+00 3.09e-01 5.20e+01 ... (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 - 0.101: 1880 0.101 - 0.202: 457 0.202 - 0.303: 62 0.303 - 0.404: 28 0.404 - 0.505: 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 -2.66 -2.16 -0.50 2.00e-01 2.50e+01 6.38e+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 -2.66 -2.22 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.78e+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: 0.650 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 44.420 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.100 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:16.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 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= 0.787 Angle : 1.985 62.518 21385 Z= 1.326 Chirality : 0.093 0.505 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.250 0.042 TRP L 276 HIS 0.013 0.003 HIS H 46 PHE 0.048 0.013 PHE D 67 TYR 0.143 0.017 TYR C 57 ARG 0.016 0.002 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.14471 ( 809) hydrogen bonds : angle 6.19379 ( 2043) metal coordination : bond 0.32596 ( 4) metal coordination : angle 14.00908 ( 6) covalent geometry : bond 0.01351 (14921) covalent geometry : angle 1.97178 (21379) *********************** 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 : 1.072 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: 0.7648 (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: 0.5697 (mmm) outliers start: 5 outliers final: 1 residues processed: 272 average time/residue: 1.6205 time to fit residues: 472.2940 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 : 1.014 ------------------------------------------------------------------------------- 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 105 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN D 106 HIS F 93 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN L 95 HIS L 113 GLN ** L 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.140172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.114506 restraints weight = 29166.075| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.31 r_work: 0.3418 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14925 Z= 0.181 Angle : 0.684 12.821 21385 Z= 0.400 Chirality : 0.039 0.151 2429 Planarity : 0.005 0.039 1708 Dihedral : 30.578 179.459 4323 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.03 % Allowed : 12.02 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.26), residues: 1009 helix: 1.93 (0.20), residues: 631 sheet: -0.58 (0.86), residues: 30 loop : -1.01 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP L 276 HIS 0.007 0.001 HIS L 268 PHE 0.007 0.001 PHE F 100 TYR 0.011 0.001 TYR F 72 ARG 0.009 0.001 ARG L 39 Details of bonding type rmsd hydrogen bonds : bond 0.04795 ( 809) hydrogen bonds : angle 3.11762 ( 2043) metal coordination : bond 0.01252 ( 4) metal coordination : angle 7.07231 ( 6) covalent geometry : bond 0.00381 (14921) covalent geometry : angle 0.67419 (21379) *********************** 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 263 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7932 (mmp) cc_final: 0.7691 (mmp) REVERT: A 105 GLU cc_start: 0.8116 (tt0) cc_final: 0.7819 (mt-10) REVERT: C 73 ASN cc_start: 0.8283 (t0) cc_final: 0.8063 (t0) REVERT: F 35 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7846 (mtp85) REVERT: F 85 ASP cc_start: 0.8387 (m-30) cc_final: 0.8067 (m-30) REVERT: G 73 ASN cc_start: 0.8298 (t0) cc_final: 0.8069 (t0) REVERT: H 76 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7379 (mtp85) REVERT: L 49 PHE cc_start: 0.7794 (m-80) cc_final: 0.7593 (m-80) REVERT: L 95 HIS cc_start: 0.7044 (m90) cc_final: 0.6693 (m90) REVERT: L 100 GLN cc_start: 0.8008 (tp-100) cc_final: 0.7319 (tp-100) REVERT: L 109 PHE cc_start: 0.6191 (t80) cc_final: 0.5708 (t80) REVERT: L 114 ASN cc_start: 0.7527 (t0) cc_final: 0.6677 (m-40) REVERT: L 205 ARG cc_start: 0.8071 (tpt170) cc_final: 0.7761 (mmm160) REVERT: L 238 ILE cc_start: 0.8132 (mp) cc_final: 0.7918 (mp) REVERT: L 249 HIS cc_start: 0.6852 (OUTLIER) cc_final: 0.6623 (t-90) REVERT: L 262 MET cc_start: 0.7087 (mmm) cc_final: 0.6297 (mmm) outliers start: 26 outliers final: 11 residues processed: 247 average time/residue: 1.5561 time to fit residues: 413.1096 Evaluate side-chains 237 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 224 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 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 92 THR Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 212 THR 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 85 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 82 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 113 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN E 39 HIS E 76 GLN ** L 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.139810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113975 restraints weight = 29160.198| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.31 r_work: 0.3407 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14925 Z= 0.172 Angle : 0.641 16.223 21385 Z= 0.369 Chirality : 0.037 0.156 2429 Planarity : 0.005 0.053 1708 Dihedral : 30.065 174.350 4320 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.15 % Allowed : 16.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.26), residues: 1009 helix: 2.25 (0.21), residues: 632 sheet: -0.29 (0.89), residues: 30 loop : -1.03 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 42 HIS 0.006 0.001 HIS L 268 PHE 0.010 0.001 PHE L 49 TYR 0.011 0.001 TYR D 37 ARG 0.009 0.001 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.04162 ( 809) hydrogen bonds : angle 2.95641 ( 2043) metal coordination : bond 0.01536 ( 4) metal coordination : angle 8.69431 ( 6) covalent geometry : bond 0.00379 (14921) covalent geometry : angle 0.62407 (21379) *********************** 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 254 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8083 (tt0) cc_final: 0.7795 (mt-10) REVERT: C 73 ASN cc_start: 0.8410 (t0) cc_final: 0.8157 (t0) REVERT: E 105 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7738 (tm-30) REVERT: F 35 ARG cc_start: 0.8247 (mtp85) cc_final: 0.7923 (mtp85) REVERT: F 85 ASP cc_start: 0.8296 (m-30) cc_final: 0.7926 (m-30) REVERT: G 73 ASN cc_start: 0.8551 (t0) cc_final: 0.8172 (t0) REVERT: H 76 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7315 (mtp85) REVERT: L 49 PHE cc_start: 0.7692 (m-80) cc_final: 0.6974 (m-80) REVERT: L 109 PHE cc_start: 0.6366 (t80) cc_final: 0.5732 (t80) REVERT: L 153 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.8005 (t) REVERT: L 180 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6686 (tt0) REVERT: L 182 ARG cc_start: 0.5943 (tpp80) cc_final: 0.5699 (tpp80) REVERT: L 205 ARG cc_start: 0.8056 (tpt170) cc_final: 0.7689 (mmm160) REVERT: L 249 HIS cc_start: 0.6962 (OUTLIER) cc_final: 0.6707 (t-90) REVERT: L 282 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7463 (pp) outliers start: 27 outliers final: 11 residues processed: 235 average time/residue: 1.6071 time to fit residues: 404.7888 Evaluate side-chains 227 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain C residue 118 LYS 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 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 180 GLU Chi-restraints excluded: chain L residue 249 HIS 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 42 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS E 76 GLN L 246 HIS ** L 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.140338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.114510 restraints weight = 28886.245| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.30 r_work: 0.3417 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14925 Z= 0.162 Angle : 0.622 11.388 21385 Z= 0.357 Chirality : 0.036 0.152 2429 Planarity : 0.004 0.044 1708 Dihedral : 29.607 173.861 4320 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.26), residues: 1009 helix: 2.35 (0.21), residues: 628 sheet: 0.16 (0.97), residues: 30 loop : -1.08 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 42 HIS 0.004 0.001 HIS L 268 PHE 0.007 0.001 PHE E 67 TYR 0.013 0.001 TYR D 37 ARG 0.009 0.001 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 809) hydrogen bonds : angle 2.86887 ( 2043) metal coordination : bond 0.01273 ( 4) metal coordination : angle 7.04615 ( 6) covalent geometry : bond 0.00358 (14921) covalent geometry : angle 0.61029 (21379) *********************** 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: 28 poor density : 218 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8120 (tt0) cc_final: 0.7833 (mt-10) REVERT: B 93 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: C 73 ASN cc_start: 0.8448 (t0) cc_final: 0.8142 (t0) REVERT: E 56 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8905 (ttmp) REVERT: E 105 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7698 (tm-30) REVERT: F 25 ASN cc_start: 0.8479 (m110) cc_final: 0.8212 (m110) REVERT: F 35 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7925 (mtp85) REVERT: F 85 ASP cc_start: 0.8202 (m-30) cc_final: 0.7790 (m-30) REVERT: G 73 ASN cc_start: 0.8628 (t0) cc_final: 0.8179 (t0) REVERT: G 77 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8531 (mtm-85) REVERT: H 76 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7338 (mtp85) REVERT: L 109 PHE cc_start: 0.6304 (t80) cc_final: 0.5648 (t80) REVERT: L 170 LYS cc_start: 0.9184 (mtpt) cc_final: 0.8919 (mtmt) REVERT: L 180 GLU cc_start: 0.6958 (tt0) cc_final: 0.6319 (tt0) REVERT: L 182 ARG cc_start: 0.5782 (tpp80) cc_final: 0.5489 (tpp80) REVERT: L 205 ARG cc_start: 0.8114 (tpt170) cc_final: 0.7700 (mmm160) REVERT: L 249 HIS cc_start: 0.7038 (OUTLIER) cc_final: 0.6734 (t-90) REVERT: L 282 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7527 (pp) outliers start: 28 outliers final: 12 residues processed: 229 average time/residue: 1.6064 time to fit residues: 393.8417 Evaluate side-chains 223 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 93 GLN Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 56 LYS 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 77 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 92 THR Chi-restraints excluded: chain L residue 149 VAL 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 43 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN L 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.141521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.115747 restraints weight = 29115.382| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.29 r_work: 0.3438 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14925 Z= 0.152 Angle : 0.610 10.786 21385 Z= 0.350 Chirality : 0.035 0.144 2429 Planarity : 0.005 0.049 1708 Dihedral : 29.359 174.209 4320 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.80 % Allowed : 20.54 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.26), residues: 1009 helix: 2.34 (0.21), residues: 634 sheet: -0.11 (0.95), residues: 30 loop : -1.12 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 42 HIS 0.005 0.001 HIS L 268 PHE 0.007 0.001 PHE E 67 TYR 0.014 0.001 TYR D 37 ARG 0.009 0.001 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 809) hydrogen bonds : angle 2.83972 ( 2043) metal coordination : bond 0.01136 ( 4) metal coordination : angle 6.59361 ( 6) covalent geometry : bond 0.00331 (14921) covalent geometry : angle 0.60036 (21379) *********************** 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 246 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8070 (tt0) cc_final: 0.7783 (mt-10) REVERT: B 93 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7872 (mp10) REVERT: C 73 ASN cc_start: 0.8471 (t0) cc_final: 0.8155 (t0) REVERT: E 105 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7671 (tm-30) REVERT: F 25 ASN cc_start: 0.8395 (m110) cc_final: 0.8120 (m110) REVERT: F 35 ARG cc_start: 0.8299 (mtp85) cc_final: 0.7968 (mtp85) REVERT: F 85 ASP cc_start: 0.8144 (m-30) cc_final: 0.7758 (m-30) REVERT: G 73 ASN cc_start: 0.8661 (t0) cc_final: 0.8206 (t0) REVERT: H 56 MET cc_start: 0.8505 (tpp) cc_final: 0.8194 (tpp) REVERT: H 76 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7334 (mtp85) REVERT: L 49 PHE cc_start: 0.7656 (m-80) cc_final: 0.7260 (t80) REVERT: L 109 PHE cc_start: 0.6325 (t80) cc_final: 0.5793 (t80) REVERT: L 205 ARG cc_start: 0.8088 (tpt170) cc_final: 0.7659 (mmm160) REVERT: L 249 HIS cc_start: 0.7120 (t-90) cc_final: 0.6874 (t-90) REVERT: L 277 ASP cc_start: 0.8227 (p0) cc_final: 0.7857 (p0) outliers start: 24 outliers final: 11 residues processed: 231 average time/residue: 1.5222 time to fit residues: 378.1615 Evaluate side-chains 219 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 206 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 93 GLN 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 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 L residue 92 THR Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.138479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.112454 restraints weight = 28935.843| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.31 r_work: 0.3385 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14925 Z= 0.183 Angle : 0.643 14.719 21385 Z= 0.363 Chirality : 0.037 0.139 2429 Planarity : 0.005 0.062 1708 Dihedral : 29.327 172.712 4320 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.62 % Allowed : 21.35 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.27), residues: 1009 helix: 2.28 (0.21), residues: 627 sheet: -0.49 (0.91), residues: 32 loop : -1.12 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 42 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE L 109 TYR 0.018 0.002 TYR D 37 ARG 0.011 0.001 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 809) hydrogen bonds : angle 2.93628 ( 2043) metal coordination : bond 0.01442 ( 4) metal coordination : angle 8.67254 ( 6) covalent geometry : bond 0.00412 (14921) covalent geometry : angle 0.62690 (21379) *********************** 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 243 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8093 (tt0) cc_final: 0.7835 (tt0) REVERT: B 93 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: C 73 ASN cc_start: 0.8637 (t0) cc_final: 0.8226 (t0) REVERT: E 56 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8954 (ttmp) REVERT: E 105 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7630 (tm-30) REVERT: F 35 ARG cc_start: 0.8320 (mtp85) cc_final: 0.8087 (mtp85) REVERT: F 85 ASP cc_start: 0.8124 (m-30) cc_final: 0.7735 (m-30) REVERT: G 73 ASN cc_start: 0.8743 (t0) cc_final: 0.8232 (t0) REVERT: H 76 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7346 (mtp85) REVERT: L 109 PHE cc_start: 0.6358 (t80) cc_final: 0.5879 (t80) REVERT: L 194 ASP cc_start: 0.7941 (p0) cc_final: 0.7571 (p0) REVERT: L 205 ARG cc_start: 0.8149 (tpt170) cc_final: 0.7685 (mmm160) REVERT: L 249 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.6941 (t-90) REVERT: L 277 ASP cc_start: 0.8344 (p0) cc_final: 0.7900 (p0) outliers start: 31 outliers final: 19 residues processed: 226 average time/residue: 1.5948 time to fit residues: 386.5438 Evaluate side-chains 225 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 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 D residue 33 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 56 LYS 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 100 VAL 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 215 THR Chi-restraints excluded: chain L residue 249 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 67 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3931 r_free = 0.3931 target = 0.138288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.112246 restraints weight = 28743.750| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.32 r_work: 0.3383 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14925 Z= 0.185 Angle : 0.646 13.552 21385 Z= 0.365 Chirality : 0.037 0.131 2429 Planarity : 0.005 0.051 1708 Dihedral : 29.238 172.427 4320 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.38 % Allowed : 22.05 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.27), residues: 1009 helix: 2.23 (0.21), residues: 628 sheet: -0.38 (0.91), residues: 32 loop : -1.07 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP L 42 HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE L 49 TYR 0.020 0.002 TYR D 37 ARG 0.012 0.001 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 809) hydrogen bonds : angle 2.96248 ( 2043) metal coordination : bond 0.01508 ( 4) metal coordination : angle 8.45522 ( 6) covalent geometry : bond 0.00417 (14921) covalent geometry : angle 0.63079 (21379) *********************** 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 233 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8098 (tt0) cc_final: 0.7833 (tt0) REVERT: B 93 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7906 (mp10) REVERT: C 73 ASN cc_start: 0.8693 (t0) cc_final: 0.8275 (t0) REVERT: C 99 ARG cc_start: 0.8423 (mmm-85) cc_final: 0.8155 (mmm-85) REVERT: E 56 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8966 (ttmp) REVERT: E 105 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7613 (tm-30) REVERT: F 35 ARG cc_start: 0.8299 (mtp85) cc_final: 0.8082 (mtp85) REVERT: F 85 ASP cc_start: 0.8120 (m-30) cc_final: 0.7740 (m-30) REVERT: G 73 ASN cc_start: 0.8768 (t0) cc_final: 0.8214 (t0) REVERT: H 76 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7316 (mtp85) REVERT: L 109 PHE cc_start: 0.6422 (t80) cc_final: 0.6027 (t80) REVERT: L 194 ASP cc_start: 0.7983 (p0) cc_final: 0.7512 (p0) REVERT: L 205 ARG cc_start: 0.8092 (tpt170) cc_final: 0.7649 (mmm160) REVERT: L 249 HIS cc_start: 0.7271 (OUTLIER) cc_final: 0.6990 (t-90) REVERT: L 277 ASP cc_start: 0.8372 (p0) cc_final: 0.8007 (p0) outliers start: 29 outliers final: 18 residues processed: 214 average time/residue: 1.6499 time to fit residues: 379.2075 Evaluate side-chains 216 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 D residue 85 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 100 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 62 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.138337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.112163 restraints weight = 28537.792| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.32 r_work: 0.3381 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14925 Z= 0.182 Angle : 0.664 15.974 21385 Z= 0.367 Chirality : 0.038 0.419 2429 Planarity : 0.005 0.068 1708 Dihedral : 29.218 172.889 4320 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.27 % Allowed : 23.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.27), residues: 1009 helix: 2.24 (0.21), residues: 628 sheet: -0.58 (0.88), residues: 32 loop : -1.11 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP L 42 HIS 0.003 0.001 HIS B 75 PHE 0.013 0.001 PHE L 49 TYR 0.022 0.002 TYR H 80 ARG 0.020 0.001 ARG L 253 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 809) hydrogen bonds : angle 2.95177 ( 2043) metal coordination : bond 0.01487 ( 4) metal coordination : angle 8.41428 ( 6) covalent geometry : bond 0.00409 (14921) covalent geometry : angle 0.64912 (21379) *********************** 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 233 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8102 (tt0) cc_final: 0.7846 (tt0) REVERT: B 93 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: C 73 ASN cc_start: 0.8742 (t0) cc_final: 0.8387 (t0) REVERT: C 99 ARG cc_start: 0.8420 (mmm-85) cc_final: 0.8157 (mmm-85) REVERT: E 56 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8999 (ttmp) REVERT: E 105 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7595 (tm-30) REVERT: F 35 ARG cc_start: 0.8285 (mtp85) cc_final: 0.8072 (mtp85) REVERT: F 85 ASP cc_start: 0.8125 (m-30) cc_final: 0.7753 (m-30) REVERT: G 73 ASN cc_start: 0.8780 (t0) cc_final: 0.8227 (t0) REVERT: H 76 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7342 (mtp85) REVERT: L 109 PHE cc_start: 0.6428 (t80) cc_final: 0.6071 (t80) REVERT: L 194 ASP cc_start: 0.7913 (p0) cc_final: 0.7552 (p0) REVERT: L 205 ARG cc_start: 0.8057 (tpt170) cc_final: 0.7608 (mmm160) REVERT: L 220 ARG cc_start: 0.7447 (mtt90) cc_final: 0.7190 (mtt90) REVERT: L 249 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.7071 (t-90) outliers start: 28 outliers final: 19 residues processed: 214 average time/residue: 1.5354 time to fit residues: 353.4331 Evaluate side-chains 225 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 D residue 33 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 100 VAL 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 149 VAL Chi-restraints excluded: chain L residue 154 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 54 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.133642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107389 restraints weight = 28267.534| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.31 r_work: 0.3304 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 14925 Z= 0.285 Angle : 0.733 16.937 21385 Z= 0.408 Chirality : 0.043 0.459 2429 Planarity : 0.006 0.068 1708 Dihedral : 29.471 172.667 4320 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.15 % Allowed : 23.57 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.27), residues: 1009 helix: 1.89 (0.21), residues: 626 sheet: -1.30 (0.82), residues: 36 loop : -1.28 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP L 42 HIS 0.003 0.001 HIS B 75 PHE 0.017 0.002 PHE L 49 TYR 0.029 0.002 TYR H 80 ARG 0.013 0.001 ARG L 253 Details of bonding type rmsd hydrogen bonds : bond 0.05430 ( 809) hydrogen bonds : angle 3.21509 ( 2043) metal coordination : bond 0.01782 ( 4) metal coordination : angle 10.23839 ( 6) covalent geometry : bond 0.00658 (14921) covalent geometry : angle 0.71281 (21379) *********************** 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 235 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8166 (tt0) cc_final: 0.7910 (tt0) REVERT: B 93 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7975 (mp10) REVERT: C 73 ASN cc_start: 0.8879 (t0) cc_final: 0.8454 (t0) REVERT: C 76 THR cc_start: 0.8841 (p) cc_final: 0.8548 (t) REVERT: E 56 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8972 (ttmp) REVERT: E 105 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7568 (tm-30) REVERT: F 35 ARG cc_start: 0.8265 (mtp85) cc_final: 0.8041 (mtp85) REVERT: F 85 ASP cc_start: 0.8239 (m-30) cc_final: 0.7837 (m-30) REVERT: G 73 ASN cc_start: 0.8810 (t0) cc_final: 0.8249 (t0) REVERT: H 76 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7348 (mtp85) REVERT: H 96 ARG cc_start: 0.8715 (tpp80) cc_final: 0.8356 (mtt-85) REVERT: L 49 PHE cc_start: 0.8092 (m-80) cc_final: 0.7664 (t80) REVERT: L 159 LEU cc_start: 0.8690 (mt) cc_final: 0.8436 (mm) REVERT: L 189 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7896 (tp30) REVERT: L 194 ASP cc_start: 0.8163 (p0) cc_final: 0.7830 (p0) REVERT: L 205 ARG cc_start: 0.8187 (tpt170) cc_final: 0.7591 (mmm160) REVERT: L 249 HIS cc_start: 0.7407 (OUTLIER) cc_final: 0.7106 (t-90) REVERT: L 282 LEU cc_start: 0.8161 (tp) cc_final: 0.7960 (tp) outliers start: 27 outliers final: 17 residues processed: 218 average time/residue: 1.4994 time to fit residues: 351.9822 Evaluate side-chains 220 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 D residue 33 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 100 VAL 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 149 VAL Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 213 LEU 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 122 optimal weight: 7.9990 chunk 102 optimal weight: 30.0000 chunk 104 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3908 r_free = 0.3908 target = 0.136399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110251 restraints weight = 28454.240| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.31 r_work: 0.3354 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14925 Z= 0.196 Angle : 0.699 18.470 21385 Z= 0.383 Chirality : 0.038 0.428 2429 Planarity : 0.005 0.047 1708 Dihedral : 29.328 173.907 4320 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.57 % Allowed : 24.97 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.27), residues: 1009 helix: 2.01 (0.21), residues: 626 sheet: -1.74 (0.75), residues: 43 loop : -1.17 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 42 HIS 0.003 0.001 HIS B 75 PHE 0.013 0.001 PHE L 49 TYR 0.027 0.002 TYR H 80 ARG 0.010 0.001 ARG L 253 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 809) hydrogen bonds : angle 3.08698 ( 2043) metal coordination : bond 0.01666 ( 4) metal coordination : angle 10.14872 ( 6) covalent geometry : bond 0.00444 (14921) covalent geometry : angle 0.67822 (21379) ********************** 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 230 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8132 (tt0) cc_final: 0.7871 (tt0) REVERT: B 93 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7937 (mp10) REVERT: C 73 ASN cc_start: 0.8809 (t0) cc_final: 0.8413 (t0) REVERT: C 76 THR cc_start: 0.8803 (p) cc_final: 0.8548 (t) REVERT: E 56 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.9007 (ttmp) REVERT: E 105 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7610 (tm-30) REVERT: F 35 ARG cc_start: 0.8255 (mtp85) cc_final: 0.8050 (mtp85) REVERT: F 85 ASP cc_start: 0.8238 (m-30) cc_final: 0.7832 (m-30) REVERT: G 73 ASN cc_start: 0.8788 (t0) cc_final: 0.8175 (t0) REVERT: H 76 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7328 (mtp85) REVERT: H 96 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8296 (mtt-85) REVERT: H 98 LEU cc_start: 0.8902 (mt) cc_final: 0.8668 (mm) REVERT: L 109 PHE cc_start: 0.6505 (t80) cc_final: 0.6002 (t80) REVERT: L 159 LEU cc_start: 0.8622 (mt) cc_final: 0.8334 (mm) REVERT: L 174 LEU cc_start: 0.8993 (mt) cc_final: 0.8710 (mt) REVERT: L 194 ASP cc_start: 0.7959 (p0) cc_final: 0.7553 (p0) REVERT: L 205 ARG cc_start: 0.8142 (tpt170) cc_final: 0.7616 (mmm160) REVERT: L 249 HIS cc_start: 0.7484 (OUTLIER) cc_final: 0.7193 (t-90) outliers start: 22 outliers final: 14 residues processed: 217 average time/residue: 1.5334 time to fit residues: 358.6823 Evaluate side-chains 223 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR 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 D residue 33 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 100 VAL 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 149 VAL Chi-restraints excluded: chain L residue 213 LEU 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 12 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.136889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.110753 restraints weight = 28854.795| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.33 r_work: 0.3365 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14925 Z= 0.188 Angle : 0.688 16.920 21385 Z= 0.378 Chirality : 0.038 0.418 2429 Planarity : 0.005 0.053 1708 Dihedral : 29.239 173.854 4320 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.22 % Allowed : 25.67 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.27), residues: 1009 helix: 2.01 (0.21), residues: 627 sheet: -1.87 (0.76), residues: 41 loop : -1.13 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP L 42 HIS 0.003 0.001 HIS B 75 PHE 0.013 0.001 PHE L 49 TYR 0.030 0.002 TYR H 80 ARG 0.013 0.001 ARG L 195 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 809) hydrogen bonds : angle 3.06043 ( 2043) metal coordination : bond 0.01465 ( 4) metal coordination : angle 9.43560 ( 6) covalent geometry : bond 0.00427 (14921) covalent geometry : angle 0.66943 (21379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10036.19 seconds wall clock time: 171 minutes 10.86 seconds (10270.86 seconds total)