Starting phenix.real_space_refine on Fri Oct 23 07:48:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/32yy_59279/10_2026/32yy_59279.cif Found real_map, /net/cci-nas-00/data/ceres_data/32yy_59279/10_2026/32yy_59279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/32yy_59279/10_2026/32yy_59279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/32yy_59279/10_2026/32yy_59279.map" model { file = "/net/cci-nas-00/data/ceres_data/32yy_59279/10_2026/32yy_59279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/32yy_59279/10_2026/32yy_59279.cif" } resolution = 3.86 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= 0.001 sd= 0.020 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 50 5.16 5 C 5601 2.51 5 N 1540 2.21 5 O 1689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8886 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1770 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 16, 'TRANS': 208} Chain breaks: 1 Chain: "B" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1770 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 16, 'TRANS': 208} Chain breaks: 1 Chain: "C" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1770 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 16, 'TRANS': 208} Chain breaks: 1 Chain: "D" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1770 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 16, 'TRANS': 208} Chain breaks: 1 Chain: "E" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1770 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 16, 'TRANS': 208} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 IHP A 501 " occ=0.00 ... (34 atoms not shown) pdb=" P6 IHP A 501 " occ=0.00 Time building chain proxies: 1.26, per 1000 atoms: 0.14 Number of scatterers: 8886 At special positions: 0 Unit cell: (113.573, 112.744, 83.729, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 6 15.00 O 1689 8.00 N 1540 7.00 C 5601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 170.1 milliseconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 64.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 29 through 44 removed outlier: 3.589A pdb=" N GLN A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 77 through 102 removed outlier: 3.515A pdb=" N GLN A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.765A pdb=" N ALA A 127 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 147 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.564A pdb=" N ARG A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.845A pdb=" N TYR A 227 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 44 removed outlier: 3.655A pdb=" N GLN B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 60 Processing helix chain 'B' and resid 64 through 76 Processing helix chain 'B' and resid 77 through 102 removed outlier: 3.722A pdb=" N ARG B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.699A pdb=" N ALA B 127 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 Processing helix chain 'B' and resid 168 through 184 removed outlier: 3.525A pdb=" N ARG B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 201 removed outlier: 3.887A pdb=" N VAL B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN B 201 " --> pdb=" O MET B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.830A pdb=" N TYR B 227 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.596A pdb=" N GLN C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 59 Processing helix chain 'C' and resid 64 through 76 removed outlier: 3.634A pdb=" N LEU C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 102 removed outlier: 3.540A pdb=" N GLN C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG C 97 " --> pdb=" O GLN C 93 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN C 99 " --> pdb=" O GLN C 95 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.513A pdb=" N LEU C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 128 removed outlier: 3.778A pdb=" N ALA C 127 " --> pdb=" O SER C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 147 Processing helix chain 'C' and resid 168 through 184 Processing helix chain 'C' and resid 186 through 201 removed outlier: 3.594A pdb=" N LYS C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN C 201 " --> pdb=" O MET C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 removed outlier: 3.558A pdb=" N ALA C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.576A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR C 227 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.657A pdb=" N GLN D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 59 Processing helix chain 'D' and resid 64 through 75 Processing helix chain 'D' and resid 77 through 102 removed outlier: 3.534A pdb=" N GLN D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG D 97 " --> pdb=" O GLN D 93 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 removed outlier: 3.510A pdb=" N LEU D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.783A pdb=" N ALA D 127 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 147 Processing helix chain 'D' and resid 168 through 184 Processing helix chain 'D' and resid 186 through 201 removed outlier: 3.970A pdb=" N VAL D 192 " --> pdb=" O LYS D 188 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TYR D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.759A pdb=" N TYR D 227 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL D 228 " --> pdb=" O ILE D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.639A pdb=" N GLN E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 77 through 102 removed outlier: 3.570A pdb=" N GLN E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E 102 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 115 Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.750A pdb=" N ALA E 127 " --> pdb=" O SER E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 147 Processing helix chain 'E' and resid 168 through 184 Processing helix chain 'E' and resid 186 through 201 removed outlier: 3.770A pdb=" N VAL E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN E 201 " --> pdb=" O MET E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 209 Processing helix chain 'E' and resid 222 through 231 removed outlier: 3.872A pdb=" N TYR E 227 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL E 228 " --> pdb=" O ILE E 224 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS E 229 " --> pdb=" O SER E 225 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA E 230 " --> pdb=" O GLU E 226 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.99 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2930 1.34 - 1.46: 1731 1.46 - 1.58: 4334 1.58 - 1.69: 6 1.69 - 1.81: 80 Bond restraints: 9081 Sorted by residual: bond pdb=" CA ASP A 109 " pdb=" CB ASP A 109 " ideal model delta sigma weight residual 1.513 1.572 -0.058 2.59e-02 1.49e+03 5.09e+00 bond pdb=" CA PHE D 158 " pdb=" CB PHE D 158 " ideal model delta sigma weight residual 1.536 1.570 -0.034 1.58e-02 4.01e+03 4.62e+00 bond pdb=" CA ASP E 109 " pdb=" CB ASP E 109 " ideal model delta sigma weight residual 1.517 1.564 -0.047 2.41e-02 1.72e+03 3.84e+00 bond pdb=" CA ASP B 109 " pdb=" CB ASP B 109 " ideal model delta sigma weight residual 1.517 1.560 -0.044 2.41e-02 1.72e+03 3.28e+00 bond pdb=" C TYR B 169 " pdb=" N PRO B 170 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.28e-02 6.10e+03 2.91e+00 ... (remaining 9076 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11929 1.92 - 3.85: 292 3.85 - 5.77: 77 5.77 - 7.70: 11 7.70 - 9.62: 6 Bond angle restraints: 12315 Sorted by residual: angle pdb=" N ILE D 210 " pdb=" CA ILE D 210 " pdb=" C ILE D 210 " ideal model delta sigma weight residual 111.91 106.43 5.48 8.90e-01 1.26e+00 3.80e+01 angle pdb=" C ASN D 107 " pdb=" N ILE D 108 " pdb=" CA ILE D 108 " ideal model delta sigma weight residual 121.97 131.03 -9.06 1.80e+00 3.09e-01 2.54e+01 angle pdb=" C ASN C 107 " pdb=" N ILE C 108 " pdb=" CA ILE C 108 " ideal model delta sigma weight residual 121.97 130.98 -9.01 1.80e+00 3.09e-01 2.51e+01 angle pdb=" N ILE D 123 " pdb=" CA ILE D 123 " pdb=" C ILE D 123 " ideal model delta sigma weight residual 113.53 109.23 4.30 9.80e-01 1.04e+00 1.92e+01 angle pdb=" N ILE A 123 " pdb=" CA ILE A 123 " pdb=" C ILE A 123 " ideal model delta sigma weight residual 113.53 109.26 4.27 9.80e-01 1.04e+00 1.90e+01 ... (remaining 12310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4781 17.92 - 35.84: 587 35.84 - 53.76: 200 53.76 - 71.68: 56 71.68 - 89.61: 13 Dihedral angle restraints: 5637 sinusoidal: 2357 harmonic: 3280 Sorted by residual: dihedral pdb=" CA ALA C 23 " pdb=" C ALA C 23 " pdb=" N ARG C 24 " pdb=" CA ARG C 24 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ALA E 23 " pdb=" C ALA E 23 " pdb=" N ARG E 24 " pdb=" CA ARG E 24 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA SER E 157 " pdb=" C SER E 157 " pdb=" N PHE E 158 " pdb=" CA PHE E 158 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 950 0.040 - 0.080: 279 0.080 - 0.120: 93 0.120 - 0.161: 11 0.161 - 0.201: 3 Chirality restraints: 1336 Sorted by residual: chirality pdb=" CB THR C 160 " pdb=" CA THR C 160 " pdb=" OG1 THR C 160 " pdb=" CG2 THR C 160 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB THR B 160 " pdb=" CA THR B 160 " pdb=" OG1 THR B 160 " pdb=" CG2 THR B 160 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CB THR E 160 " pdb=" CA THR E 160 " pdb=" OG1 THR E 160 " pdb=" CG2 THR E 160 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 1333 not shown) Planarity restraints: 1600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 158 " -0.012 2.00e-02 2.50e+03 1.76e-02 5.45e+00 pdb=" CG PHE D 158 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE D 158 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE D 158 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE D 158 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 158 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 158 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 158 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C PHE D 158 " 0.034 2.00e-02 2.50e+03 pdb=" O PHE D 158 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN D 159 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 109 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" CG ASP D 109 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP D 109 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP D 109 " -0.010 2.00e-02 2.50e+03 ... (remaining 1597 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3009 2.85 - 3.36: 8829 3.36 - 3.88: 13919 3.88 - 4.39: 14711 4.39 - 4.90: 25024 Nonbonded interactions: 65492 Sorted by model distance: nonbonded pdb=" OD1 ASP A 109 " pdb=" N ALA A 110 " model vdw 2.341 3.120 nonbonded pdb=" OD1 ASP E 109 " pdb=" N ALA E 110 " model vdw 2.476 3.120 nonbonded pdb=" O ASP B 67 " pdb=" OD1 ASP B 67 " model vdw 2.536 3.040 nonbonded pdb=" OD1 ASP B 109 " pdb=" N ALA B 110 " model vdw 2.540 3.120 nonbonded pdb=" N ILE D 210 " pdb=" N LYS D 211 " model vdw 2.570 2.560 ... (remaining 65487 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' and resid 1 through 235) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.120 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.003 0.058 9081 Z= 0.154 Angle : 0.772 9.620 12315 Z= 0.437 Chirality : 0.042 0.201 1336 Planarity : 0.005 0.037 1600 Dihedral : 18.600 89.605 3507 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.43 % Favored : 93.12 % Rotamer: Outliers : 2.89 % Allowed : 33.92 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.25), residues: 1105 helix: 0.57 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -1.42 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 24 TYR 0.022 0.001 TYR C 199 PHE 0.040 0.002 PHE D 158 TRP 0.006 0.001 TRP D 68 HIS 0.001 0.001 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 9081) covalent geometry : angle 0.77217 / 0.44 (12315) hydrogen bonds : bond 0.25632 / 17.15 ( 447) hydrogen bonds : angle 7.55026 / 5.42 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.3901 (tmm) cc_final: 0.1806 (mmm) REVERT: A 95 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: A 109 ASP cc_start: 0.8401 (t0) cc_final: 0.8152 (t0) REVERT: B 95 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: B 176 LEU cc_start: 0.8508 (mt) cc_final: 0.7977 (tt) REVERT: B 214 LYS cc_start: 0.7902 (mmmt) cc_final: 0.7549 (mtmt) REVERT: C 7 MET cc_start: 0.5432 (ppp) cc_final: 0.4282 (mmm) REVERT: C 95 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: C 119 ASN cc_start: 0.8597 (p0) cc_final: 0.8277 (p0) REVERT: D 176 LEU cc_start: 0.8781 (mt) cc_final: 0.8273 (tt) REVERT: E 7 MET cc_start: 0.5371 (ppp) cc_final: 0.4841 (mmt) REVERT: E 95 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7515 (tm-30) outliers start: 28 outliers final: 23 residues processed: 201 average time/residue: 0.0750 time to fit residues: 20.0551 Evaluate side-chains 205 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 61 HIS Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0170 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN D 95 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** 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 = 0.4107 r_free = 0.4107 target = 0.186192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.159256 restraints weight = 12659.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.162767 restraints weight = 8510.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.165240 restraints weight = 6469.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.166712 restraints weight = 5343.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.167916 restraints weight = 4720.499| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9081 Z= 0.128 Angle : 0.613 8.173 12315 Z= 0.316 Chirality : 0.042 0.143 1336 Planarity : 0.005 0.028 1600 Dihedral : 8.414 58.408 1303 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.33 % Favored : 92.22 % Rotamer: Outliers : 5.57 % Allowed : 28.04 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.26), residues: 1105 helix: 1.27 (0.20), residues: 695 sheet: None (None), residues: 0 loop : -1.95 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 98 TYR 0.011 0.001 TYR E 199 PHE 0.028 0.002 PHE D 158 TRP 0.006 0.001 TRP B 145 HIS 0.001 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9081) covalent geometry : angle 0.61273 / 0.32 (12315) hydrogen bonds : bond 0.03805 / 2.47 ( 447) hydrogen bonds : angle 4.54946 / 3.27 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.4011 (tmm) cc_final: 0.3509 (tmm) REVERT: A 90 ASP cc_start: 0.8352 (t70) cc_final: 0.7944 (t0) REVERT: A 95 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: B 95 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: B 176 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8156 (tt) REVERT: C 7 MET cc_start: 0.5565 (ppp) cc_final: 0.4332 (mmm) REVERT: C 95 GLN cc_start: 0.8619 (tm-30) cc_final: 0.7699 (tm-30) REVERT: C 119 ASN cc_start: 0.8635 (p0) cc_final: 0.8263 (p0) REVERT: C 176 LEU cc_start: 0.8641 (mt) cc_final: 0.8367 (tt) REVERT: C 200 GLU cc_start: 0.6625 (tp30) cc_final: 0.5471 (tm-30) REVERT: D 95 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: D 176 LEU cc_start: 0.8801 (mt) cc_final: 0.8343 (tt) REVERT: D 187 GLU cc_start: 0.7350 (tp30) cc_final: 0.7150 (tp30) REVERT: E 7 MET cc_start: 0.5362 (ppp) cc_final: 0.4969 (mmm) REVERT: E 95 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7411 (tm-30) REVERT: E 222 ASP cc_start: 0.7617 (t0) cc_final: 0.7323 (t70) outliers start: 54 outliers final: 37 residues processed: 239 average time/residue: 0.0992 time to fit residues: 32.3025 Evaluate side-chains 230 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 61 HIS Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 224 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [36, 19, 52, 74, 50, 28, 77, 13, 29, 34, 57] chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN D 95 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** 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 = 0.4043 r_free = 0.4043 target = 0.179812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.152715 restraints weight = 12840.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.156154 restraints weight = 8707.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.158303 restraints weight = 6649.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.160013 restraints weight = 5576.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.160983 restraints weight = 4914.822| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9081 Z= 0.164 Angle : 0.621 8.392 12315 Z= 0.319 Chirality : 0.043 0.143 1336 Planarity : 0.004 0.027 1600 Dihedral : 7.543 59.759 1282 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.24 % Favored : 92.31 % Rotamer: Outliers : 7.01 % Allowed : 28.04 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.26), residues: 1105 helix: 1.37 (0.20), residues: 695 sheet: None (None), residues: 0 loop : -2.12 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.011 0.001 TYR D 199 PHE 0.012 0.002 PHE C 172 TRP 0.011 0.001 TRP D 120 HIS 0.001 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 9081) covalent geometry : angle 0.62104 / 0.32 (12315) hydrogen bonds : bond 0.03906 / 2.55 ( 447) hydrogen bonds : angle 4.40512 / 3.18 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 200 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.4084 (tmm) cc_final: 0.2129 (mmm) REVERT: C 7 MET cc_start: 0.5493 (ppp) cc_final: 0.4236 (mmm) REVERT: C 95 GLN cc_start: 0.8652 (tm-30) cc_final: 0.7761 (tm-30) REVERT: C 176 LEU cc_start: 0.8671 (mt) cc_final: 0.8466 (tt) REVERT: C 224 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.7912 (mp) REVERT: D 36 MET cc_start: 0.8224 (tpp) cc_final: 0.7982 (tpp) REVERT: D 95 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: E 7 MET cc_start: 0.5490 (ppp) cc_final: 0.5022 (mmt) REVERT: E 222 ASP cc_start: 0.7815 (t0) cc_final: 0.7576 (t70) outliers start: 68 outliers final: 45 residues processed: 247 average time/residue: 0.0973 time to fit residues: 32.5529 Evaluate side-chains 234 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 61 HIS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 224 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [96, 75, 23, 80, 41, 30, 61, 7, 85, 87, 79] chunk 96 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 chunk 30 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 85 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN B 46 ASN B 95 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN D 95 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 99 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.177922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.150060 restraints weight = 12923.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.153645 restraints weight = 8473.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.156114 restraints weight = 6344.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.157737 restraints weight = 5207.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.158527 restraints weight = 4547.115| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9081 Z= 0.110 Angle : 0.564 8.288 12315 Z= 0.291 Chirality : 0.042 0.140 1336 Planarity : 0.004 0.046 1600 Dihedral : 6.095 58.954 1263 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.24 % Favored : 92.31 % Rotamer: Outliers : 5.98 % Allowed : 29.18 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.26), residues: 1105 helix: 1.70 (0.21), residues: 690 sheet: None (None), residues: 0 loop : -1.96 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 24 TYR 0.013 0.001 TYR C 199 PHE 0.012 0.001 PHE E 158 TRP 0.011 0.001 TRP B 120 HIS 0.001 0.000 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9081) covalent geometry : angle 0.56438 / 0.29 (12315) hydrogen bonds : bond 0.02951 / 1.92 ( 447) hydrogen bonds : angle 4.07383 / 2.94 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 193 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8441 (t70) cc_final: 0.8019 (t0) REVERT: A 95 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: A 176 LEU cc_start: 0.8627 (mt) cc_final: 0.8061 (tt) REVERT: A 224 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8283 (mt) REVERT: B 176 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7929 (tt) REVERT: B 200 GLU cc_start: 0.6867 (tp30) cc_final: 0.5606 (tm-30) REVERT: C 7 MET cc_start: 0.5509 (ppp) cc_final: 0.4180 (mmm) REVERT: C 95 GLN cc_start: 0.8557 (tm-30) cc_final: 0.7685 (tm-30) REVERT: C 176 LEU cc_start: 0.8509 (mt) cc_final: 0.8249 (tt) REVERT: C 200 GLU cc_start: 0.6905 (tp30) cc_final: 0.5780 (tm-30) REVERT: D 95 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: D 176 LEU cc_start: 0.8648 (mt) cc_final: 0.8214 (tt) REVERT: E 7 MET cc_start: 0.5409 (ppp) cc_final: 0.4864 (mmm) REVERT: E 222 ASP cc_start: 0.7890 (t0) cc_final: 0.7646 (t70) outliers start: 58 outliers final: 45 residues processed: 238 average time/residue: 0.0930 time to fit residues: 30.2254 Evaluate side-chains 239 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 61 HIS Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 142 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [79, 72, 8, 104, 35, 16, 66, 85, 103, 96, 53] chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN B 46 ASN B 99 ASN C 46 ASN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.176462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.148880 restraints weight = 12914.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.152304 restraints weight = 8535.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154720 restraints weight = 6432.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.156370 restraints weight = 5299.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.157385 restraints weight = 4633.033| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9081 Z= 0.122 Angle : 0.581 8.809 12315 Z= 0.298 Chirality : 0.042 0.139 1336 Planarity : 0.004 0.043 1600 Dihedral : 5.955 59.414 1261 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.88 % Favored : 92.67 % Rotamer: Outliers : 6.80 % Allowed : 28.97 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.26), residues: 1105 helix: 1.68 (0.21), residues: 695 sheet: None (None), residues: 0 loop : -1.98 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 98 TYR 0.014 0.001 TYR D 199 PHE 0.010 0.002 PHE E 158 TRP 0.008 0.001 TRP B 120 HIS 0.001 0.000 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 9081) covalent geometry : angle 0.58084 / 0.30 (12315) hydrogen bonds : bond 0.02935 / 1.90 ( 447) hydrogen bonds : angle 4.03937 / 2.91 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 191 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.4019 (tmm) cc_final: 0.3615 (tmm) REVERT: A 90 ASP cc_start: 0.8371 (t70) cc_final: 0.7950 (t0) REVERT: A 176 LEU cc_start: 0.8707 (mt) cc_final: 0.8176 (tt) REVERT: A 224 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8365 (mt) REVERT: B 200 GLU cc_start: 0.6793 (tp30) cc_final: 0.5554 (tm-30) REVERT: C 7 MET cc_start: 0.5621 (ppp) cc_final: 0.4278 (mmm) REVERT: C 95 GLN cc_start: 0.8555 (tm-30) cc_final: 0.7715 (tm-30) REVERT: C 176 LEU cc_start: 0.8592 (mt) cc_final: 0.8325 (tt) REVERT: C 200 GLU cc_start: 0.6780 (tp30) cc_final: 0.5725 (tm-30) REVERT: D 24 ARG cc_start: 0.7893 (mmt-90) cc_final: 0.7681 (mmt180) REVERT: D 36 MET cc_start: 0.8265 (tpp) cc_final: 0.8037 (tpp) REVERT: D 176 LEU cc_start: 0.8742 (mt) cc_final: 0.8305 (tt) REVERT: E 7 MET cc_start: 0.5467 (ppp) cc_final: 0.4828 (mmm) REVERT: E 200 GLU cc_start: 0.7417 (tp30) cc_final: 0.6092 (tm-30) outliers start: 66 outliers final: 53 residues processed: 243 average time/residue: 0.0951 time to fit residues: 31.7160 Evaluate side-chains 240 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 186 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 61 HIS Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 224 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [61, 39, 1, 32, 65, 8, 55, 37, 56, 46, 90] chunk 61 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.131082 restraints weight = 13268.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.134337 restraints weight = 9121.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.136474 restraints weight = 7046.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.137893 restraints weight = 5930.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.138893 restraints weight = 5274.436| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 9081 Z= 0.370 Angle : 0.852 8.479 12315 Z= 0.437 Chirality : 0.051 0.146 1336 Planarity : 0.005 0.033 1600 Dihedral : 7.046 57.961 1261 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.05 % Favored : 89.68 % Rotamer: Outliers : 8.87 % Allowed : 28.76 % Favored : 62.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.24), residues: 1105 helix: 0.45 (0.19), residues: 695 sheet: None (None), residues: 0 loop : -2.42 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 51 TYR 0.013 0.002 TYR C 25 PHE 0.019 0.003 PHE B 81 TRP 0.015 0.003 TRP E 145 HIS 0.004 0.001 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00892 / 0.37 ( 9081) covalent geometry : angle 0.85163 / 0.44 (12315) hydrogen bonds : bond 0.05394 / 3.52 ( 447) hydrogen bonds : angle 5.15806 / 3.73 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 188 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.4530 (tmm) cc_final: 0.2707 (mmp) REVERT: A 95 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: A 120 TRP cc_start: 0.7901 (m100) cc_final: 0.7425 (m100) REVERT: C 7 MET cc_start: 0.5650 (OUTLIER) cc_final: 0.4555 (mmm) REVERT: C 95 GLN cc_start: 0.8773 (tm-30) cc_final: 0.7779 (tm-30) REVERT: C 224 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8210 (mp) REVERT: D 24 ARG cc_start: 0.8398 (mmt-90) cc_final: 0.8179 (mmt180) REVERT: D 36 MET cc_start: 0.8255 (tpp) cc_final: 0.8034 (tpp) REVERT: D 200 GLU cc_start: 0.8092 (tp30) cc_final: 0.7850 (tp30) REVERT: D 214 LYS cc_start: 0.8320 (tppt) cc_final: 0.8053 (tppp) REVERT: E 7 MET cc_start: 0.5819 (ppp) cc_final: 0.5102 (mmm) outliers start: 86 outliers final: 57 residues processed: 253 average time/residue: 0.1024 time to fit residues: 35.0337 Evaluate side-chains 234 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 174 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 61 HIS Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 154 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [50, 100, 38, 47, 74, 15, 109, 66, 88, 39, 96] chunk 50 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN D 46 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.165836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137849 restraints weight = 13029.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.141196 restraints weight = 8651.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.143586 restraints weight = 6530.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145023 restraints weight = 5381.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146168 restraints weight = 4741.801| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9081 Z= 0.124 Angle : 0.619 8.397 12315 Z= 0.318 Chirality : 0.043 0.151 1336 Planarity : 0.005 0.035 1600 Dihedral : 6.478 59.992 1261 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.42 % Favored : 92.31 % Rotamer: Outliers : 6.08 % Allowed : 31.86 % Favored : 62.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.26), residues: 1105 helix: 1.32 (0.20), residues: 695 sheet: None (None), residues: 0 loop : -2.19 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 24 TYR 0.024 0.001 TYR D 199 PHE 0.011 0.001 PHE E 158 TRP 0.021 0.001 TRP B 120 HIS 0.002 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 9081) covalent geometry : angle 0.61875 / 0.32 (12315) hydrogen bonds : bond 0.02982 / 1.94 ( 447) hydrogen bonds : angle 4.21985 / 3.05 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 179 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 95 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8085 (tm-30) REVERT: A 176 LEU cc_start: 0.8691 (mt) cc_final: 0.8035 (tt) REVERT: B 46 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.7876 (m110) REVERT: B 176 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7985 (tt) REVERT: C 7 MET cc_start: 0.5387 (OUTLIER) cc_final: 0.4465 (mmm) REVERT: C 95 GLN cc_start: 0.8633 (tm-30) cc_final: 0.7748 (tm-30) REVERT: C 197 MET cc_start: 0.8845 (tpp) cc_final: 0.8605 (tpp) REVERT: D 176 LEU cc_start: 0.8659 (mt) cc_final: 0.8247 (tt) REVERT: E 7 MET cc_start: 0.5605 (ppp) cc_final: 0.5066 (mmm) REVERT: E 46 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8150 (m110) REVERT: E 222 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7272 (t70) outliers start: 59 outliers final: 45 residues processed: 225 average time/residue: 0.1002 time to fit residues: 30.7667 Evaluate side-chains 216 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 165 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 222 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [94, 65, 103, 36, 90, 47, 12, 24, 88, 13, 67] chunk 94 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN B 46 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN D 46 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.165007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.138029 restraints weight = 12999.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.141217 restraints weight = 8945.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.143406 restraints weight = 6908.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144903 restraints weight = 5790.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.145917 restraints weight = 5118.155| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9081 Z= 0.237 Angle : 0.734 9.445 12315 Z= 0.370 Chirality : 0.047 0.224 1336 Planarity : 0.005 0.069 1600 Dihedral : 6.598 59.658 1259 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.23 % Favored : 90.50 % Rotamer: Outliers : 6.91 % Allowed : 32.27 % Favored : 60.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.25), residues: 1105 helix: 1.01 (0.20), residues: 695 sheet: None (None), residues: 0 loop : -2.31 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 24 TYR 0.010 0.001 TYR C 25 PHE 0.024 0.002 PHE D 158 TRP 0.017 0.002 TRP A 120 HIS 0.002 0.001 HIS C 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.24 ( 9081) covalent geometry : angle 0.73408 / 0.37 (12315) hydrogen bonds : bond 0.04004 / 2.61 ( 447) hydrogen bonds : angle 4.51362 / 3.25 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 176 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.4381 (tmm) cc_final: 0.2589 (mmm) REVERT: A 224 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8429 (mp) REVERT: B 41 LYS cc_start: 0.8334 (tptt) cc_final: 0.7885 (tmmt) REVERT: B 197 MET cc_start: 0.8712 (tpp) cc_final: 0.8411 (mmm) REVERT: C 7 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.4630 (mmm) REVERT: C 95 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8103 (tm-30) REVERT: D 176 LEU cc_start: 0.8783 (mt) cc_final: 0.8374 (tt) REVERT: E 7 MET cc_start: 0.5591 (ppp) cc_final: 0.5099 (mmm) REVERT: E 222 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7281 (t70) outliers start: 67 outliers final: 53 residues processed: 230 average time/residue: 0.1015 time to fit residues: 31.4621 Evaluate side-chains 221 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 165 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 203 ASN Chi-restraints excluded: chain E residue 222 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [89, 45, 38, 16, 72, 50, 66, 81, 64, 34, 105] chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 0.0070 chunk 34 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN B 46 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN D 46 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.171817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146076 restraints weight = 12554.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.149759 restraints weight = 7903.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.152278 restraints weight = 5722.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154005 restraints weight = 4575.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155002 restraints weight = 3920.803| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9081 Z= 0.126 Angle : 0.643 9.178 12315 Z= 0.329 Chirality : 0.044 0.224 1336 Planarity : 0.005 0.060 1600 Dihedral : 6.370 59.837 1259 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.15 % Favored : 92.58 % Rotamer: Outliers : 5.36 % Allowed : 33.61 % Favored : 61.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.26), residues: 1105 helix: 1.65 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -2.17 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 24 TYR 0.020 0.001 TYR D 199 PHE 0.013 0.001 PHE E 158 TRP 0.016 0.002 TRP B 120 HIS 0.001 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9081) covalent geometry : angle 0.64282 / 0.33 (12315) hydrogen bonds : bond 0.02940 / 1.91 ( 447) hydrogen bonds : angle 4.11681 / 2.96 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.4316 (tmm) cc_final: 0.2509 (mmm) REVERT: A 95 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: B 176 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8092 (tt) REVERT: C 7 MET cc_start: 0.5531 (OUTLIER) cc_final: 0.4580 (mmm) REVERT: C 95 GLN cc_start: 0.8563 (tm-30) cc_final: 0.7742 (tm-30) REVERT: C 197 MET cc_start: 0.8794 (tpp) cc_final: 0.8591 (tpp) REVERT: D 176 LEU cc_start: 0.8693 (mt) cc_final: 0.8306 (tt) REVERT: E 46 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.8101 (m110) outliers start: 52 outliers final: 38 residues processed: 219 average time/residue: 0.0999 time to fit residues: 29.5453 Evaluate side-chains 219 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [77, 41, 38, 11, 87, 2, 26, 10, 73, 45, 75] chunk 77 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 0.0670 chunk 2 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN D 46 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.173972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.146855 restraints weight = 12857.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.150473 restraints weight = 8367.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.152946 restraints weight = 6216.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.154638 restraints weight = 5088.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155737 restraints weight = 4418.546| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9081 Z= 0.128 Angle : 0.676 12.357 12315 Z= 0.339 Chirality : 0.044 0.224 1336 Planarity : 0.005 0.055 1600 Dihedral : 6.258 58.856 1259 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.60 % Favored : 92.13 % Rotamer: Outliers : 4.43 % Allowed : 34.74 % Favored : 60.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.26), residues: 1105 helix: 1.75 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -2.08 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 24 TYR 0.019 0.001 TYR A 199 PHE 0.012 0.001 PHE E 158 TRP 0.016 0.001 TRP C 120 HIS 0.001 0.000 HIS D 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 9081) covalent geometry : angle 0.67571 / 0.34 (12315) hydrogen bonds : bond 0.02865 / 1.87 ( 447) hydrogen bonds : angle 4.03987 / 2.91 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.4164 (tmm) cc_final: 0.2362 (mmm) REVERT: A 75 SER cc_start: 0.8829 (t) cc_final: 0.8617 (t) REVERT: A 95 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: A 224 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8280 (mt) REVERT: B 176 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8113 (tt) REVERT: C 7 MET cc_start: 0.5523 (OUTLIER) cc_final: 0.4588 (mmm) REVERT: C 95 GLN cc_start: 0.8531 (tm-30) cc_final: 0.7683 (tm-30) REVERT: D 75 SER cc_start: 0.8807 (t) cc_final: 0.8605 (t) REVERT: D 176 LEU cc_start: 0.8685 (mt) cc_final: 0.8273 (tt) outliers start: 43 outliers final: 35 residues processed: 211 average time/residue: 0.1005 time to fit residues: 28.4834 Evaluate side-chains 214 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [2, 87, 60, 64, 26, 98, 101, 92, 12, 30, 105] chunk 2 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN C 46 ASN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.170000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143414 restraints weight = 12797.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146640 restraints weight = 8755.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.148874 restraints weight = 6722.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.150134 restraints weight = 5596.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.151367 restraints weight = 4984.592| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9081 Z= 0.174 Angle : 0.690 8.683 12315 Z= 0.350 Chirality : 0.045 0.225 1336 Planarity : 0.005 0.052 1600 Dihedral : 6.377 59.740 1259 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.14 % Favored : 91.58 % Rotamer: Outliers : 5.26 % Allowed : 34.43 % Favored : 60.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.26), residues: 1105 helix: 1.64 (0.20), residues: 685 sheet: None (None), residues: 0 loop : -2.18 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 24 TYR 0.016 0.001 TYR C 199 PHE 0.010 0.002 PHE E 158 TRP 0.015 0.002 TRP C 120 HIS 0.001 0.001 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 ( 9081) covalent geometry : angle 0.69043 / 0.35 (12315) hydrogen bonds : bond 0.03303 / 2.16 ( 447) hydrogen bonds : angle 4.18791 / 3.02 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1467.24 seconds wall clock time: 26 minutes 1.27 seconds (1561.27 seconds total)